count: 798
list:
- accessibility: Open access
  additionDate: '2016-03-24T16:22:28Z'
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  biotoolsID: repet
  collectionID:
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  - elixir-fr-sdp-2019
  - URGI
  confidence_flag: tool
  cost: Free of charge
  credit:
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    fundrefid: null
    gridid: null
    name: URGI
    note: 'This tool has a "Numero de depot APP": FR 001 480007 000 R P 2008 000 31
      235'
    orcidid: null
    rorid: null
    typeEntity: Institute
    typeRole:
    - Developer
    - Contributor
    - Maintainer
    - Provider
    - Support
    - Documentor
    url: http://urgi.versailles.inrae.fr/
  description: "The REPET package integrates bioinformatics pipelines dedicated to\
    \ detect, annotate and analyze transposable elements (TEs) in genomic sequences.\
    \ The main pipelines are (i) TEdenovo, which search for interspersed repeats,\
    \ build consensus sequences and classify them according to TE features, and (ii)\n\
    \ TEannot, which mines a genome with a library of TE sequences, for instance the\
    \ one produced by the TEdenovo pipeline, to provide TE annotations exported into\
    \ GFF3 files."
  documentation:
  - note: see also https://urgi.versailles.inrae.fr/Tools/REPET/README
    type:
    - General
    url: https://urgi.versailles.inrae.fr/Tools/REPET
  - note: null
    type:
    - Installation instructions
    url: https://urgi.versailles.inrae.fr/Tools/REPET/INSTALL
  - note: See also https://urgi.versailles.inra.fr/Tools/REPET/TEannot-tuto
    type:
    - User manual
    url: https://urgi.versailles.inrae.fr/Tools/REPET/TEdenovo-tuto
  - note: null
    type:
    - Training material
    url: https://forgemia.inra.fr/urgi-anagen/wiki-repet/-/wikis/REPET-V3.0-tutorial
  download:
  - note: null
    type: Source code
    url: https://urgi.versailles.inrae.fr/download/repet/REPET_linux-x64-3.0.tar.gz
    version: v3.0
  editPermission:
    authors:
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    - johann_confais
    - raphael.flores
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    type: group
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  elixirNode:
  - France
  elixirPlatform:
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  elixir_badge: 0
  function:
  - cmd: null
    input:
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        term: DNA sequence
        uri: http://edamontology.org/data_3494
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
    note: null
    operation:
    - term: Repeat sequence detection
      uri: http://edamontology.org/operation_0379
    - term: Repeat sequence analysis
      uri: http://edamontology.org/operation_0237
    output:
    - data:
        term: DNA sequence
        uri: http://edamontology.org/data_3494
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
    - data:
        term: Feature table
        uri: http://edamontology.org/data_1270
      format:
      - term: Sequence feature table format (text)
        uri: http://edamontology.org/format_2206
    - data:
        term: Annotation track
        uri: http://edamontology.org/data_3002
      format:
      - term: GFF3-seq
        uri: http://edamontology.org/format_1939
  homepage: https://urgi.versailles.inrae.fr/Tools/REPET
  homepage_status: 0
  language:
  - C++
  - Python
  lastUpdate: '2025-09-09T08:10:41.737859Z'
  license: CECILL-2.0
  link:
  - note: null
    type:
    - Repository
    url: https://urgi.versailles.inrae.fr/download/repet/
  maturity: Legacy
  name: REPET
  operatingSystem:
  - Linux
  - Mac
  otherID: []
  owner: Institut Francais de Bioinform
  publication:
  - doi: 10.1371/journal.pone.0091929
    metadata:
      abstract: ''
      authors: []
      citationCount: 226
      date: '2014-05-02T00:00:00Z'
      journal: PLoS ONE
      title: 'PASTEC: An automatic transposable element classification tool'
    note: null
    pmcid: PMC4008368
    pmid: '24786468'
    type:
    - Primary
    version: null
  - doi: 10.1371/journal.pone.0016526
    metadata:
      abstract: ''
      authors: []
      citationCount: 355
      date: '2011-02-09T00:00:00Z'
      journal: PLoS ONE
      title: Considering transposable element diversification in de novo annotation
        approaches
    note: null
    pmcid: PMC3031573
    pmid: '21304975'
    type:
    - Primary
    version: null
  - doi: 10.1371/journal.pcbi.0010022
    metadata:
      abstract: ''
      authors: []
      citationCount: 279
      date: '2005-01-01T00:00:00Z'
      journal: PLoS Computational Biology
      title: Combined evidence annotation of transposable elements in genome sequences
    note: null
    pmcid: PMC1185648
    pmid: '16110336'
    type:
    - Primary
    version: null
  - doi: 10.1007/s00239-003-0007-2
    metadata:
      abstract: ''
      authors: []
      citationCount: 65
      date: '2003-12-29T00:00:00Z'
      journal: Journal of Molecular Evolution
      title: Detection of New Transposable Element Families in Drosophila melanogaster
        and Anopheles gambiae Genomes
    note: null
    pmcid: null
    pmid: '15008403'
    type:
    - Method
    version: null
  - doi: 10.1109/JPROC.2016.2590833
    metadata:
      abstract: ''
      authors: []
      citationCount: 18
      date: '2017-03-01T00:00:00Z'
      journal: Proceedings of the IEEE
      title: 'De Novo Annotation of Transposable Elements: Tackling the Fat Genome
        Issue'
    note: null
    pmcid: null
    pmid: null
    type:
    - Method
    version: null
  relation: []
  toolType:
  - Command-line tool
  topic:
  - term: Sequence composition, complexity and repeats
    uri: http://edamontology.org/topic_0157
  - term: DNA
    uri: http://edamontology.org/topic_0654
  - term: Nucleic acid structure analysis
    uri: http://edamontology.org/topic_0097
  validated: 1
  version:
  - v3.0
- accessibility: Open access
  additionDate: '2019-02-13T17:01:40Z'
  biotoolsCURIE: biotools:Jalview
  biotoolsID: Jalview
  collectionID:
  - ELIXIR-UK
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: null
    fundrefid: null
    gridid: null
    name: Jim Procter
    note: null
    orcidid: https://orcid.org/0000-0002-7865-7382
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: http://www.lifesci.dundee.ac.uk/people/jim-procter
  - email: null
    fundrefid: null
    gridid: null
    name: Geoff Barton
    note: null
    orcidid: https://orcid.org/0000-0002-9014-5355
    rorid: null
    typeEntity: null
    typeRole: []
    url: https://www.lifesci.dundee.ac.uk/people/geoff-barton
  description: Jalview is a free cross-platform program for multiple sequence alignment
    editing, visualisation and analysis. Use it to align, view and edit sequence alignments,
    analyse them with phylogenetic trees and principal components analysis (PCA) plots
    and explore molecular structures and annotation.
  documentation:
  - note: null
    type:
    - Citation instructions
    url: https://www.jalview.org/about/citation
  - note: Hands-on exercises, Training courses and Training videos
    type:
    - Training material
    url: https://www.jalview.org/training/
  - note: null
    type:
    - FAQ
    url: https://www.jalview.org/help/faq
  - note: null
    type:
    - User manual
    url: https://www.jalview.org/help/documentation/
  download:
  - note: null
    type: Downloads page
    url: https://www.jalview.org/download
    version: null
  - note: null
    type: Source code
    url: https://www.jalview.org/download/source/
    version: null
  - note: Binaries for all platforms
    type: Binaries
    url: https://www.jalview.org/download/?os=all
    version: null
  - note: null
    type: Icon
    url: https://www.jalview.org/favicon.svg
    version: null
  - note: Executable JAR file
    type: Binaries
    url: https://www.jalview.org/download/other/jar/
    version: null
  editPermission:
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    - jimprocter
    type: group
  elixirCommunity: []
  elixirNode:
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  elixirPlatform:
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  - Interoperability
  elixir_badge: 0
  function:
  - cmd: null
    input:
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        term: Sequence alignment
        uri: http://edamontology.org/data_0863
      format:
      - term: GFF3-seq
        uri: http://edamontology.org/format_1939
      - term: ClustalW format
        uri: http://edamontology.org/format_1982
      - term: Stockholm format
        uri: http://edamontology.org/format_1961
      - term: FASTA-aln
        uri: http://edamontology.org/format_1984
      - term: GFF2-seq
        uri: http://edamontology.org/format_1938
      - term: FASTA
        uri: http://edamontology.org/format_1929
      - term: nbrf/pir
        uri: http://edamontology.org/format_1948
      - term: BioJSON (Jalview)
        uri: http://edamontology.org/format_3774
      - term: PHYLIP format
        uri: http://edamontology.org/format_1997
      - term: BLC
        uri: http://edamontology.org/format_3313
      - term: RNAML
        uri: http://edamontology.org/format_3311
      - term: GCG MSF
        uri: http://edamontology.org/format_1947
      - term: Pileup
        uri: http://edamontology.org/format_3015
      - term: mmCIF
        uri: http://edamontology.org/format_1477
      - term: VCF
        uri: http://edamontology.org/format_3016
      - term: Format
        uri: http://edamontology.org/format_1915
    - data:
        term: Structure alignment
        uri: http://edamontology.org/data_0886
      format:
      - term: PDB
        uri: http://edamontology.org/format_1476
    note: 'Other Input formats:

      AMSA (.amsa);

      JnetFile (.concise, .jnet);

      PFAM (.pfam);

      Substitution matrix (.matrix);

      Jalview Project File (.jvp);

      Jalview Feature File (.features, .jvfeatures);

      Jalview Annotations File (.annotations, .jvannotations);

      Predicted Aligned Error (PAE) Matrix File (.json)

      ...

      Other Output formats:

      PFAM (.pfam);

      BioJS (.biojs) (interactive HTML/Javascript);

      Jalview Project File (.jvp);'
    operation:
    - term: Sequence visualisation
      uri: http://edamontology.org/operation_0564
    - term: Phylogenetic tree analysis
      uri: http://edamontology.org/operation_0324
    - term: Sequence alignment editing
      uri: http://edamontology.org/operation_3081
    output:
    - data:
        term: Sequence alignment
        uri: http://edamontology.org/data_0863
      format:
      - term: nbrf/pir
        uri: http://edamontology.org/format_1948
      - term: JSON
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      - term: Stockholm format
        uri: http://edamontology.org/format_1961
      - term: FASTA
        uri: http://edamontology.org/format_1929
      - term: PHYLIP format
        uri: http://edamontology.org/format_1997
      - term: BLC
        uri: http://edamontology.org/format_3313
      - term: BioJSON (Jalview)
        uri: http://edamontology.org/format_3774
      - term: GCG MSF
        uri: http://edamontology.org/format_1947
      - term: Pileup
        uri: http://edamontology.org/format_3015
      - term: ClustalW format
        uri: http://edamontology.org/format_1982
    - data:
        term: Plot
        uri: http://edamontology.org/data_2884
      format:
      - term: PNG
        uri: http://edamontology.org/format_3603
      - term: HTML
        uri: http://edamontology.org/format_2331
      - term: EPS
        uri: http://edamontology.org/format_3466
      - term: SVG
        uri: http://edamontology.org/format_3604
      - term: Format
        uri: http://edamontology.org/format_1915
  homepage: https://www.jalview.org/
  homepage_status: 0
  language: []
  lastUpdate: '2025-09-04T13:26:28.643607Z'
  license: GPL-3.0
  link:
  - note: null
    type:
    - Discussion forum
    url: https://discourse.jalview.org/
  - note: null
    type:
    - Issue tracker
    url: https://issues.jalview.org/
  - note: Latest development version
    type:
    - Other
    url: https://www.jalview.org/development/jalview_develop/
  - note: null
    type:
    - Repository
    url: https://source.jalview.org/crucible/browse/jalview
  - note: Twitter feed
    type:
    - Social media
    url: https://twitter.com/Jalview
  - note: YouTube training videos
    type:
    - Social media
    url: https://www.youtube.com/channel/UCIjpnvZB770yz7ftbrJ0tfw
  maturity: Mature
  name: Jalview
  operatingSystem:
  - Linux
  - Windows
  - Mac
  otherID: []
  owner: ben_s
  publication:
  - doi: 10.1093/bioinformatics/btp033
    metadata:
      abstract: ''
      authors: []
      citationCount: 7499
      date: '2009-05-07T00:00:00Z'
      journal: Bioinformatics
      title: Jalview Version 2-A multiple sequence alignment editor and analysis workbench
    note: null
    pmcid: PMC2672624
    pmid: '19151095'
    type: []
    version: null
  relation:
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    type: uses
  - biotoolsID: chimera
    type: uses
  - biotoolsID: chimerax
    type: uses
  - biotoolsID: pymol
    type: uses
  - biotoolsID: bioconda
    type: includedIn
  - biotoolsID: 3d-beacons
    type: uses
  - biotoolsID: uniprot
    type: uses
  - biotoolsID: pfam
    type: uses
  - biotoolsID: ensembl
    type: uses
  - biotoolsID: pdb
    type: uses
  - biotoolsID: rfam
    type: uses
  toolType:
  - Desktop application
  - Command-line tool
  topic:
  - term: Sequence analysis
    uri: http://edamontology.org/topic_0080
  - term: Data visualisation
    uri: http://edamontology.org/topic_0092
  validated: 1
  version:
  - 2.11.5.0
- accessibility: Open access
  additionDate: '2021-05-08T17:25:21Z'
  biotoolsCURIE: biotools:bakta
  biotoolsID: bakta
  collectionID: []
  confidence_flag: tool
  cost: Free of charge
  credit:
  - email: oliver.schwengers@cb.jlug.de
    fundrefid: null
    gridid: null
    name: Oliver Schwengers
    note: null
    orcidid: https://orcid.org/0000-0003-4216-2721
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    - Developer
    - Maintainer
    url: https://github.com/oschwengers
  - email: null
    fundrefid: null
    gridid: null
    name: Justus Liebig University Giessen
    note: null
    orcidid: null
    rorid: null
    typeEntity: Institute
    typeRole:
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    url: https://www.uni-giessen.de
  description: Rapid & standardized annotation of bacterial genomes, MAGs & plasmids
  documentation:
  - note: null
    type:
    - General
    url: https://github.com/oschwengers/bakta/blob/main/README.md
  - note: null
    type:
    - Contributions policy
    url: https://github.com/oschwengers/bakta/blob/main/CONTRIBUTION.md
  - note: null
    type:
    - Code of conduct
    url: https://github.com/oschwengers/bakta/blob/main/CODE_OF_CONDUCT.md
  - note: null
    type:
    - User manual
    url: https://bakta.readthedocs.io/
  download:
  - note: Mandatory annotation database
    type: Other
    url: https://zenodo.org/records/14916843
    version: v6.0
  editPermission:
    authors:
    - ELIXIR-CZ
    - bebatut
    type: group
  elixirCommunity: []
  elixirNode:
  - Germany
  elixirPlatform:
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  elixir_badge: 0
  function:
  - cmd: bakta --db <db-path> --prefix <prefix> --output <output-path> genome.fasta
    input:
    - data:
        term: Sequence assembly
        uri: http://edamontology.org/data_0925
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
    - data:
        term: Sequence features metadata
        uri: http://edamontology.org/data_2914
      format:
      - term: TSV
        uri: http://edamontology.org/format_3475
    - data:
        term: Sequence coordinates
        uri: http://edamontology.org/data_2012
      format:
      - term: GFF3
        uri: http://edamontology.org/format_1975
    - data:
        term: Protein sequence record
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      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
    - data:
        term: Hidden Markov model
        uri: http://edamontology.org/data_1364
      format:
      - term: HMMER3
        uri: http://edamontology.org/format_3329
    note: null
    operation:
    - term: Genome annotation
      uri: http://edamontology.org/operation_0362
    output:
    - data:
        term: Feature table
        uri: http://edamontology.org/data_1270
      format:
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        uri: http://edamontology.org/format_1936
      - term: EMBL format
        uri: http://edamontology.org/format_1927
      - term: GFF3
        uri: http://edamontology.org/format_1975
      - term: JSON
        uri: http://edamontology.org/format_3464
      - term: TSV
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    - data:
        term: Protein sequence record
        uri: http://edamontology.org/data_2886
      format:
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        uri: http://edamontology.org/format_1929
    - data:
        term: Nucleic acid sequence record
        uri: http://edamontology.org/data_2887
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
    - data:
        term: Plot
        uri: http://edamontology.org/data_2884
      format:
      - term: PNG
        uri: http://edamontology.org/format_3603
      - term: SVG
        uri: http://edamontology.org/format_3604
    - data:
        term: Score
        uri: http://edamontology.org/data_1772
      format:
      - term: TSV
        uri: http://edamontology.org/format_3475
  homepage: https://github.com/oschwengers/bakta
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2025-09-01T07:59:35.735958Z'
  license: GPL-3.0
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/oschwengers/bakta
  - note: null
    type:
    - Issue tracker
    url: https://github.com/oschwengers/bakta/issues
  - note: null
    type:
    - Other
    url: https://bioconda.github.io/recipes/bakta/README.html
  - note: null
    type:
    - Service
    url: https://bakta.computational.bio
  maturity: Mature
  name: Bakta
  operatingSystem:
  - Linux
  - Mac
  otherID: []
  owner: oschwengers
  publication:
  - doi: 10.1099/mgen.0.000685
    metadata:
      abstract: ''
      authors: []
      citationCount: 582
      date: '2021-01-01T00:00:00Z'
      journal: Microbial Genomics
      title: 'Bakta: Rapid and standardized annotation of bacterial genomes via alignment-free
        sequence identification'
    note: null
    pmcid: PMC8743544
    pmid: '34739369'
    type:
    - Primary
    version: '1.1'
  relation:
  - biotoolsID: diamond
    type: uses
  - biotoolsID: hmmer3
    type: uses
  - biotoolsID: infernal
    type: uses
  - biotoolsID: trnascan-se
    type: uses
  - biotoolsID: blast
    type: uses
  - biotoolsID: aragorn
    type: uses
  - biotoolsID: pilercr
    type: uses
  - biotoolsID: deepsig
    type: uses
  toolType:
  - Command-line tool
  - Web application
  topic:
  - term: Genomics
    uri: http://edamontology.org/topic_0622
  - term: Sequence analysis
    uri: http://edamontology.org/topic_0080
  - term: Bioinformatics
    uri: http://edamontology.org/topic_0091
  validated: 0
  version:
  - v1.11.4
- accessibility: Open access
  additionDate: '2016-12-19T14:27:26Z'
  biotoolsCURIE: biotools:fqcleaner
  biotoolsID: fqcleaner
  collectionID:
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  - Institut Pasteur
  - fqtools
  confidence_flag: null
  cost: null
  credit:
  - email: galaxy@pasteur.fr
    fundrefid: null
    gridid: null
    name: Galaxy Support Team
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: null
  description: Mini workflow for preprocessing fastq files, it includes quality trimming,
    duplicate and artefacts filters for FASTQ read files.
  documentation: []
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Data
        uri: http://edamontology.org/data_0006
      format:
      - term: FASTQ
        uri: http://edamontology.org/format_1930
    - data:
        term: Data
        uri: http://edamontology.org/data_0006
      format:
      - term: FASTQ
        uri: http://edamontology.org/format_1930
    - data:
        term: Data
        uri: http://edamontology.org/data_0006
      format:
      - term: FASTQ
        uri: http://edamontology.org/format_1930
    - data:
        term: Sequence alignment
        uri: http://edamontology.org/data_0863
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
    note: null
    operation:
    - term: Sequence trimming
      uri: http://edamontology.org/operation_3192
    - term: Data filtering
      uri: http://edamontology.org/operation_3695
    output:
    - data:
        term: Data
        uri: http://edamontology.org/data_0006
      format:
      - term: FASTQ-sanger
        uri: http://edamontology.org/format_1932
    - data:
        term: Data
        uri: http://edamontology.org/data_0006
      format:
      - term: FASTQ-sanger
        uri: http://edamontology.org/format_1932
    - data:
        term: Data
        uri: http://edamontology.org/data_0006
      format:
      - term: FASTQ-sanger
        uri: http://edamontology.org/format_1932
  homepage: https://gensoft.pasteur.fr/docs/fqCleanER/21.10/
  homepage_status: 0
  language: []
  lastUpdate: '2025-08-27T10:47:14.412802Z'
  license: null
  link:
  - note: null
    type:
    - Galaxy service
    url: https://galaxy.pasteur.fr/tool_runner?tool_id=toolshed.pasteur.fr/repos/odoppelt/fqcleaner/fqCleaner/0.4.1.1
  maturity: Mature
  name: fqcleaner
  operatingSystem: []
  otherID: []
  owner: hmenager
  publication:
  - doi: 10.1093/nar/gkw343
    metadata:
      abstract: High-throughput data production technologies, particularly ‘next-generation’
        DNA sequencing, have ushered in widespread and disruptive changes to biomedical
        research. Making sense of the large datasets produced by these technologies
        requires sophisticated statistical and computational methods, as well as substantial
        computational power. This has led to an acute crisis in life sciences, as
        researchers without informatics training attempt to perform computation-dependent
        analyses. Since 2005, the Galaxy project has worked to address this problem
        by providing a framework that makes advanced computational tools usable by
        non experts. Galaxy seeks to make data-intensive research more accessible,
        transparent and reproducible by providing a Web-based environment in which
        users can perform computational analyses and have all of the details automatically
        tracked for later inspection, publication, or reuse. In this report we highlight
        recently added features enabling biomedical analyses on a large scale.
      authors:
      - name: Afgan E.
      - name: Baker D.
      - name: van den Beek M.
      - name: Blankenberg D.
      - name: Bouvier D.
      - name: Cech M.
      - name: Chilton J.
      - name: Clements D.
      - name: Coraor N.
      - name: Eberhard C.
      - name: Gruning B.
      - name: Guerler A.
      - name: Hillman-Jackson J.
      - name: Kuster G.V.
      - name: Rasche E.
      - name: Soranzo N.
      - name: Turaga N.
      - name: Taylor J.
      - name: Nekrutenko A.
      - name: Goecks J.
      citationCount: 1477
      date: '2016-07-08T00:00:00Z'
      journal: Nucleic Acids Research
      title: 'The Galaxy platform for accessible, reproducible and collaborative biomedical
        analyses: 2016 update'
    note: null
    pmcid: null
    pmid: null
    type:
    - Other
    version: null
  - doi: 10.7490/f1000research.1114334.1
    metadata: null
    note: null
    pmcid: null
    pmid: null
    type:
    - Other
    version: null
  relation: []
  toolType:
  - Web application
  topic:
  - term: Sequencing
    uri: http://edamontology.org/topic_3168
  - term: Data quality management
    uri: http://edamontology.org/topic_3572
  - term: Sequence analysis
    uri: http://edamontology.org/topic_0080
  validated: 1
  version:
  - 0.4.1.1
- accessibility: Open access
  additionDate: '2025-07-23T10:27:57.572501Z'
  biotoolsCURIE: biotools:etenlnc
  biotoolsID: etenlnc
  collectionID: []
  confidence_flag: tool
  cost: Free of charge
  credit:
  - email: barah@tezu.ernet.in
    fundrefid: null
    gridid: null
    name: Pankaj Barah
    note: Assistant Professor at Department of Molecular Biology and Biotechnology,
      Tezpur University.
    orcidid: https://orcid.org/0000-0001-7039-7996
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    - Maintainer
    url: https://www.tezu.ernet.in/dmbbt/profile/34
  - email: prangannathofficial@gmai.com
    fundrefid: null
    gridid: null
    name: Prangan Nath
    note: null
    orcidid: https://orcid.org/0000-0002-9451-7822
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    - Maintainer
    url: null
  description: ETENLNC (End-To-End-Novel-NonCoding) is a lncRNA identification and
    analysis framework
  documentation:
  - note: A detailed guide on running ETENLNC using the demo data can be found in
      the ETENLNC manual (supplementary to our publication)
    type:
    - Command-line options
    url: https://github.com/EvolOMICS-TU/ETENLNC
  download:
  - note: Sample/demo data for ETENLNC. A detailed guide on running ETENLNC using
      the demo data can be found in the ETENLNC manual (supplementary to our publication).
    type: Biological data
    url: https://zenodo.org/records/14325721?token=eyJhbGciOiJIUzUxMiJ9.eyJpZCI6ImVmYTllNWJkLWE4ODUtNGM3OC05YTAxLWM4ZDk5YTljZDZjMCIsImRhdGEiOnt9LCJyYW5kb20iOiI4M2I1YjBlZDQ4MmUyZTIxNDg2YmI0YTFkMWE5MTI1OCJ9.HeB3WrsPduNzMyXjH4x5HfCgmIp4NzYv0P_11XU9lcXC_ZxEaVndP-kD0LDkxwufHVNlroeAhdK33PR51F6jnw
    version: '1.0'
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: bash ETENLNC_docker.sh
    input:
    - data:
        term: Expression data
        uri: http://edamontology.org/data_2603
      format:
      - term: FASTQ
        uri: http://edamontology.org/format_1930
    - data:
        term: Nucleic acid sequence
        uri: http://edamontology.org/data_2977
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
    - data:
        term: Genome map
        uri: http://edamontology.org/data_1288
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
    - data:
        term: Annotation track
        uri: http://edamontology.org/data_3002
      format:
      - term: GTF
        uri: http://edamontology.org/format_2306
      - term: GFF
        uri: http://edamontology.org/format_2305
    note: Run ETENLNC on paired-end raw RNA-Seq (.fastq) data
    operation:
    - term: Read pre-processing
      uri: http://edamontology.org/operation_3219
    - term: Sequencing quality control
      uri: http://edamontology.org/operation_3218
    - term: Transcriptome assembly
      uri: http://edamontology.org/operation_3258
    - term: Nucleic acid feature detection
      uri: http://edamontology.org/operation_0415
    - term: RNA-Seq quantification
      uri: http://edamontology.org/operation_3800
    - term: Differential gene expression profiling
      uri: http://edamontology.org/operation_3223
    - term: Heat map generation
      uri: http://edamontology.org/operation_0531
    - term: RNA secondary structure prediction
      uri: http://edamontology.org/operation_0278
    - term: k-mer counting
      uri: http://edamontology.org/operation_3472
    - term: Protein-nucleic acid interaction analysis
      uri: http://edamontology.org/operation_0389
    - term: RNA-binding protein prediction
      uri: http://edamontology.org/operation_3901
    - term: Gene regulatory network prediction
      uri: http://edamontology.org/operation_2437
    output:
    - data:
        term: Nucleic acid sequence record
        uri: http://edamontology.org/data_2887
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
    - data:
        term: Gene expression matrix
        uri: http://edamontology.org/data_3112
      format:
      - term: CSV
        uri: http://edamontology.org/format_3752
    - data:
        term: Heat map
        uri: http://edamontology.org/data_1636
      format:
      - term: PDF
        uri: http://edamontology.org/format_3508
    - data:
        term: Protein interaction data
        uri: http://edamontology.org/data_0906
      format: []
  homepage: https://github.com/EvolOMICS-TU/ETENLNC
  homepage_status: 0
  language: []
  lastUpdate: '2025-07-23T10:27:57.574879Z'
  license: GPL-3.0
  link:
  - note: GitHub Repo
    type:
    - Repository
    url: https://github.com/EvolOMICS-TU/ETENLNC
  maturity: Emerging
  name: ETENLNC
  operatingSystem:
  - Linux
  - Mac
  - Windows
  otherID: []
  owner: prangannath
  publication:
  - doi: 10.1016/j.compbiolchem.2024.108140
    metadata:
      abstract: 'Long non-coding RNAs (lncRNAs) play crucial roles in the regulation
        of gene expression and maintenance of genomic integrity through various interactions
        with DNA, RNA, and proteins. The availability of large-scale sequence data
        from various high-throughput platforms has opened possibilities to identify,
        predict, and functionally annotate lncRNAs. As a result, there is a growing
        demand for an integrative computational framework capable of identifying known
        lncRNAs, predicting novel lncRNAs, and inferring the downstream regulatory
        interactions of lncRNAs at the genome-scale. We present ETENLNC (End-To-End-Novel-Long-NonCoding),
        a user-friendly, integrative, open-source, scalable, and modular computational
        framework for identifying and analyzing lncRNAs from raw RNA-Seq data. ETENLNC
        employs six stringent filtration steps to identify novel lncRNAs, performs
        differential expression analysis of mRNA and lncRNA transcripts, and predicts
        regulatory interactions between lncRNAs, mRNAs, miRNAs, and proteins. We benchmarked
        ETENLNC against six existing tools and optimized it for desktop workstations
        and high-performance computing environments using data from three different
        species. ETENLNC is freely available on GitHub: https://github.com/EvolOMICS-TU/ETENLNC.'
      authors:
      - name: Nath P.
      - name: Bhuyan K.
      - name: Bhattacharyya D.K.
      - name: Barah P.
      citationCount: 2
      date: '2024-10-01T00:00:00Z'
      journal: Computational Biology and Chemistry
      title: 'ETENLNC: An end to end lncRNA identification and analysis framework
        to facilitate construction of known and novel lncRNA regulatory networks'
    note: null
    pmcid: null
    pmid: '38996755'
    type:
    - Primary
    version: '.0'
  relation:
  - biotoolsID: hisat2
    type: uses
  - biotoolsID: salmon
    type: uses
  - biotoolsID: fastqc
    type: uses
  - biotoolsID: fastp
    type: uses
  - biotoolsID: stringtie
    type: uses
  - biotoolsID: gffcompare
    type: uses
  - biotoolsID: cpc2
    type: uses
  - biotoolsID: ncbi_blast_plus
    type: uses
  - biotoolsID: tximport
    type: uses
  - biotoolsID: deseq2
    type: uses
  - biotoolsID: lnctar
    type: uses
  - biotoolsID: capsule-lpi
    type: uses
  - biotoolsID: seekr
    type: uses
  toolType:
  - Command-line tool
  topic:
  - term: Functional, regulatory and non-coding RNA
    uri: http://edamontology.org/topic_0659
  validated: 0
  version:
  - '1.0'
- accessibility: Open access
  additionDate: '2016-02-09T13:19:44Z'
  biotoolsCURIE: biotools:mirgen
  biotoolsID: mirgen
  collectionID:
  - UiO tools
  - ELIXIR-NO
  - ELIXIR-Norway
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: BastianFromm@gmail.com
    fundrefid: null
    gridid: null
    name: Bastian Fromm
    note: null
    orcidid: https://orcid.org/0000-0003-0352-3037
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    - Developer
    - Maintainer
    - Support
    url: null
  - email: kevin.j.peterson@dartmouth.edu
    fundrefid: null
    gridid: null
    name: Kevin J. Peterson
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    - Maintainer
    url: null
  - email: support@elixir.no
    fundrefid: null
    gridid: null
    name: The Norwegian Bioinformatics Platform (ELIXIR-Norway) Helpdesk
    note: null
    orcidid: null
    rorid: null
    typeEntity: Consortium
    typeRole:
    - Support
    url: https://elixir.no/helpdesk
  - email: null
    fundrefid: 10.13039/501100005366
    gridid: grid.5510.1
    name: University of Oslo
    note: null
    orcidid: null
    rorid: 01xtthb56
    typeEntity: Institute
    typeRole:
    - Provider
    url: https://www.uio.no/english/index.html
  description: MirGeneDB is a database of manually curated microRNA genes that have
    been validated and annotated as initially described in Fromm et al. 2015 , Fromm
    et al. 2020 and Fromm et al 2022. MirGeneDB 3.0 (Clarke and Hoye et al. 2024 )
    includes more than 21,000 microRNA gene entries representing more than 1,700 microRNA
    families from 114 metazoan species. All microRNAs can be browsed, searched and
    downloaded.
  documentation:
  - note: null
    type:
    - General
    url: https://www.mirgenedb.org/information
  download:
  - note: Sequence downloads for 75 species
    type: Biological data
    url: https://www.mirgenedb.org/download
    version: '3.0'
  editPermission:
    authors:
    - eca008
    type: group
  elixirCommunity: []
  elixirNode:
  - Norway
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Sequence accession (nucleic acid)
        uri: http://edamontology.org/data_1097
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
    - data:
        term: Organism identifier
        uri: http://edamontology.org/data_1869
      format: []
    note: 'Data retrieval: curated miRNA. Organism identifier: a specific miRNA identifier
      or a species  for all miRNAs for that species. Gene transcript report: with
      metadata and visualization. RNA secondary structure: the hairpin loop of the
      miRNA with bases.'
    operation:
    - term: Data retrieval
      uri: http://edamontology.org/operation_2422
    - term: Sequence visualisation
      uri: http://edamontology.org/operation_0564
    output:
    - data:
        term: Gene transcript report
        uri: http://edamontology.org/data_3134
      format:
      - term: HTML
        uri: http://edamontology.org/format_2331
    - data:
        term: RNA secondary structure
        uri: http://edamontology.org/data_0880
      format:
      - term: HTML
        uri: http://edamontology.org/format_2331
  - cmd: null
    input:
    - data:
        term: Sequence accession (nucleic acid)
        uri: http://edamontology.org/data_1097
      format: []
    note: null
    operation:
    - term: Query and retrieval
      uri: http://edamontology.org/operation_0224
    output:
    - data:
        term: RNA sequence
        uri: http://edamontology.org/data_3495
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
    - data:
        term: Sequence coordinates
        uri: http://edamontology.org/data_2012
      format:
      - term: GFF
        uri: http://edamontology.org/format_2305
      - term: BED
        uri: http://edamontology.org/format_3003
    - data:
        term: Count matrix
        uri: http://edamontology.org/data_3917
      format:
      - term: Textual format
        uri: http://edamontology.org/format_2330
  homepage: http://mirgenedb.org/
  homepage_status: 0
  language: []
  lastUpdate: '2025-07-05T22:33:30.082420Z'
  license: CC0-1.0
  link:
  - note: null
    type:
    - Helpdesk
    url: https://elixir.no/helpdesk
  maturity: Mature
  name: MirGeneDB
  operatingSystem:
  - Linux
  - Windows
  - Mac
  otherID:
  - type: doi
    value: doi:10.25504/FAIRsharing.QXSgvF
    version: '2.0'
  owner: UiO
  publication:
  - doi: 10.1093/nar/gkab1101
    metadata:
      abstract: We describe an update of MirGeneDB, the manually curated microRNA
        gene database. Adhering to uniform and consistent criteria for microRNA annotation
        and nomenclature, we substantially expanded MirGeneDB with 30 additional species
        representing previously missing metazoan phyla such as sponges, jellyfish,
        rotifers and flatworms. MirGeneDB 2.1 now consists of 75 species spanning
        over ∼800 million years of animal evolution, and contains a total number of
        16 670 microRNAs from 1549 families. Over 6000 microRNAs were added in this
        update using ∼550 datasets with ∼7.5 billion sequencing reads. By adding new
        phylogenetically important species, especially those relevant for the study
        of whole genome duplication events, and through updating evolutionary nodes
        of origin for many families and genes, we were able to substantially refine
        our nomenclature system. All changes are traceable in the specifically developed
        MirGeneDB version tracker. The performance of read-pages is improved and microRNA
        expression matrices for all tissues and species are now also downloadable.
        Altogether, this update represents a significant step toward a complete sampling
        of all major metazoan phyla, and a widely needed foundation for comparative
        microRNA genomics and transcriptomics studies. MirGeneDB 2.1 is part of RNAcentral
        and Elixir Norway, publicly and freely available at http://www.mirgenedb.org/.
      authors:
      - name: Fromm B.
      - name: Hoye E.
      - name: Domanska D.
      - name: Zhong X.
      - name: Aparicio-Puerta E.
      - name: Ovchinnikov V.
      - name: Umu S.U.
      - name: Chabot P.J.
      - name: Kang W.
      - name: Aslanzadeh M.
      - name: Tarbier M.
      - name: Marmol-Sanchez E.
      - name: Urgese G.
      - name: Johansen M.
      - name: Hovig E.
      - name: Hackenberg M.
      - name: Friedlander M.R.
      - name: Peterson K.J.
      citationCount: 95
      date: '2022-01-07T00:00:00Z'
      journal: Nucleic Acids Research
      title: 'MirGeneDB 2.1: Toward a complete sampling of all major animal phyla'
    note: null
    pmcid: PMC8728216
    pmid: '34850127'
    type:
    - Primary
    version: '2.1'
  - doi: 10.1093/nar/gkz885
    metadata:
      abstract: Small non-coding RNAs have gained substantial attention due to their
        roles in animal development and human disorders. Among them, microRNAs are
        special because individual gene sequences are conserved across the animal
        kingdom. In addition, unique and mechanistically well understood features
        can clearly distinguish bona fide miRNAs from the myriad other small RNAs
        generated by cells. However, making this distinction is not a common practice
        and, thus, not surprisingly, the heterogeneous quality of available miRNA
        complements has become a major concern in microRNA research. We addressed
        this by extensively expanding our curated microRNA gene database-MirGeneDB-to
        45 organisms, encompassing a wide phylogenetic swath of animal evolution.
        By consistently annotating and naming 10,899 microRNA genes in these organisms,
        we show that previous microRNA annotations contained not only many false positives,
        but surprisingly lacked >2000 bona fide microRNAs. Indeed, curated microRNA
        complements of closely related organisms are very similar and can be used
        to reconstruct ancestral miRNA repertoires. MirGeneDB represents a robust
        platform for microRNA-based research, providing deeper and more significant
        insights into the biology and evolution of miRNAs as well as biomedical and
        biomarker research. MirGeneDB is publicly and freely available at http://mirgenedb.org/.
      authors:
      - name: Fromm B.
      - name: Domanska D.
      - name: Hoye E.
      - name: Ovchinnikov V.
      - name: Kang W.
      - name: Aparicio-Puerta E.
      - name: Johansen M.
      - name: Flatmark K.
      - name: Mathelier A.
      - name: Hovig E.
      - name: Hackenberg M.
      - name: Friedlander M.R.
      - name: Peterson K.J.
      citationCount: 178
      date: '2020-01-01T00:00:00Z'
      journal: Nucleic Acids Research
      title: 'MirGeneDB 2.0: The metazoan microRNA complement'
    note: null
    pmcid: PMC6943042
    pmid: '31598695'
    type:
    - Primary
    version: '2.0'
  - doi: 10.1146/annurev-genet-120213-092023
    metadata:
      abstract: Although microRNAs (miRNAs) are among the most intensively studied
        molecules of the past 20 years, determining what is and what is not a miRNA
        has not been straightforward. Here, we present a uniform system for the annotation
        and nomenclature of miRNA genes. We show that less than a third of the 1,881
        human miRBase entries, and only approximately 16% of the 7,095 metazoan miRBase
        entries, are robustly supported as miRNA genes. Furthermore, we show that
        the human repertoire of miRNAs has been shaped by periods of intense miRNA
        innovation and that mature gene products show a very different tempo and mode
        of sequence evolution than star products. We establish a new open access database-MirGeneDB
        (http://mirgenedb.org)-to catalog this set of miRNAs, which complements the
        efforts of miRBase but differs from it by annotating the mature versus star
        products and by imposing an evolutionary hierarchy upon this curated and consistently
        named repertoire.
      authors:
      - name: Fromm B.
      - name: Billipp T.
      - name: Peck L.E.
      - name: Johansen M.
      - name: Tarver J.E.
      - name: King B.L.
      - name: Newcomb J.M.
      - name: Sempere L.F.
      - name: Flatmark K.
      - name: Hovig E.
      - name: Peterson K.J.
      citationCount: 435
      date: '2015-11-23T00:00:00Z'
      journal: Annual Review of Genetics
      title: A Uniform System for the Annotation of Vertebrate microRNA Genes and
        the Evolution of the Human microRNAome
    note: null
    pmcid: PMC4743252
    pmid: '26473382'
    type:
    - Primary
    version: '1.0'
  - doi: 10.1093/nar/gkae1094
    metadata:
      abstract: We present a major update of MirGeneDB (3.0), the manually curated
        animal microRNA gene database. Beyond moving to a new server and the creation
        of a computational mirror, we have expanded the database with the addition
        of 33 invertebrate species, including representatives of 5 previously unsampled
        phyla, and 6 mammal species. MirGeneDB now contains entries for 21 822 microRNA
        genes (5160 of these from the new species) belonging to 1743 microRNA families.
        The inclusion of these new species allowed us to refine both the evolutionary
        node of appearance of a number of microRNA genes/families, as well as MirGeneDB's
        phylogenetically informed nomenclature system. Updated covariance models of
        all microRNA families, along with all smallRNA read data are now downloadable.
        These enhanced annotations will allow researchers to analyze microRNA properties
        such as secondary structure and features of their biogenesis within a robust
        phylogenetic context and without the database plagued with numerous false
        positives and false negatives. In light of these improvements, MirGeneDB 3.0
        will assume the responsibility for naming conserved novel metazoan microRNAs.
        MirGeneDB is part of RNAcentral and Elixir Norway and is publicly and freely
        available at mirgenedb.org.
      authors:
      - name: Clarke A.W.
      - name: Hoye E.
      - name: Hembrom A.A.
      - name: Paynter V.M.
      - name: Vinther J.
      - name: Wyrozemski L.
      - name: Biryukova I.
      - name: Formaggioni A.
      - name: Ovchinnikov V.
      - name: Herlyn H.
      - name: Pierce A.
      - name: Wu C.
      - name: Aslanzadeh M.
      - name: Cheneby J.
      - name: Martinez P.
      - name: Friedlander M.R.
      - name: Hovig E.
      - name: Hackenberg M.
      - name: Umu S.U.
      - name: Johansen M.
      - name: Peterson K.J.
      - name: Fromm B.
      citationCount: 6
      date: '2025-01-06T00:00:00Z'
      journal: Nucleic Acids Research
      title: 'MirGeneDB 3.0: Improved taxonomic sampling, uniform nomenclature of
        novel conserved microRNA families and updated covariance models'
    note: null
    pmcid: PMC11701709
    pmid: '39673268'
    type:
    - Primary
    version: '3.0'
  relation: []
  toolType:
  - Database portal
  topic:
  - term: Functional, regulatory and non-coding RNA
    uri: http://edamontology.org/topic_0659
  - term: Gene regulation
    uri: http://edamontology.org/topic_0204
  - term: Evolutionary biology
    uri: http://edamontology.org/topic_3299
  - term: Zoology
    uri: http://edamontology.org/topic_3500
  - term: Human biology
    uri: http://edamontology.org/topic_2815
  validated: 1
  version:
  - '3.0'
- accessibility: null
  additionDate: '2020-01-14T08:51:14Z'
  biotoolsCURIE: biotools:RepeatModeler2
  biotoolsID: RepeatModeler2
  collectionID: []
  confidence_flag: tool
  cost: Free of charge
  credit: []
  description: RepeatModeler is a de novo transposable element (TE) family identification
    and modeling package. At the heart of RepeatModeler are three de-novo repeat finding
    programs ( RECON, RepeatScout and LtrHarvest/Ltr_retriever ) which employ complementary
    computational methods for identifying repeat element boundaries and family relationships
    from sequence data.
  documentation: []
  download: []
  editPermission:
    authors: []
    type: public
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: DNA sequence
        uri: http://edamontology.org/data_3494
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
    note: null
    operation:
    - term: Genome assembly
      uri: http://edamontology.org/operation_0525
    - term: de Novo sequencing
      uri: http://edamontology.org/operation_3644
    - term: Genome annotation
      uri: http://edamontology.org/operation_0362
    output: []
  homepage: https://github.com/Dfam-consortium/RepeatModeler
  homepage_status: 0
  language:
  - Perl
  lastUpdate: '2025-07-01T04:28:03.302129Z'
  license: OSL-2.0
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/Dfam-consortium/RepeatModeler/blob/master/LICENSE
  maturity: Mature
  name: RepeatModeler2
  operatingSystem:
  - Mac
  - Linux
  otherID: []
  owner: Pub2Tools
  publication:
  - doi: 10.1101/856591
    metadata: null
    note: null
    pmcid: null
    pmid: null
    type: []
    version: null
  relation:
  - biotoolsID: repeatmodeler
    type: isNewVersionOf
  toolType:
  - Command-line tool
  topic:
  - term: Model organisms
    uri: http://edamontology.org/topic_0621
  - term: Sequence composition, complexity and repeats
    uri: http://edamontology.org/topic_0157
  - term: Whole genome sequencing
    uri: http://edamontology.org/topic_3673
  - term: Sequence assembly
    uri: http://edamontology.org/topic_0196
  - term: Mobile genetic elements
    uri: http://edamontology.org/topic_0798
  validated: 1
  version:
  - 2.0.7
- accessibility: Open access
  additionDate: '2019-11-14T18:08:10Z'
  biotoolsCURIE: biotools:purge_dups
  biotoolsID: purge_dups
  collectionID:
  - ONTeater
  confidence_flag: tool
  cost: Free of charge
  credit:
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    fundrefid: null
    gridid: null
    name: Dengfeng Guan
    note: null
    orcidid: https://orcid.org/0000-0002-6376-3940
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    url: https://www.chatlink.com.cn
  description: 'Identifying and removing haplotypic duplication in primary genome
    assemblies | haplotypic duplication identification tool | scripts/pd_config.py:
    script to generate a configuration file used by run_purge_dups.py | purge haplotigs
    and overlaps in an assembly based on read depth | Given a primary assembly pri_asm
    and an alternative assembly hap_asm (optional, if you have one), follow the steps
    shown below to build your own purge_dups pipeline, steps with same number can
    be run simultaneously. Among all the steps, although step 4 is optional, we highly
    recommend our users to do so, because assemblers may produce overrepresented seqeuences.
    In such a case, The final step 4 can be applied to remove those seqeuences'
  documentation: []
  download: []
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  function:
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    input:
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        term: Sequence set (nucleic acid)
        uri: http://edamontology.org/data_1234
      format:
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        uri: http://edamontology.org/format_1930
    - data:
        term: Sequence set (nucleic acid)
        uri: http://edamontology.org/data_1234
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
    note: null
    operation:
    - term: Genome assembly
      uri: http://edamontology.org/operation_0525
    - term: Read binning
      uri: http://edamontology.org/operation_3798
    - term: Scaffolding
      uri: http://edamontology.org/operation_3216
    output:
    - data:
        term: Sequence set (nucleic acid)
        uri: http://edamontology.org/data_1234
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
  homepage: https://github.com/dfguan/purge_dups
  homepage_status: 0
  language:
  - Python
  - C
  lastUpdate: '2025-06-30T15:34:51.626796Z'
  license: MIT
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/dfguan/purge_dups
  - note: null
    type:
    - Issue tracker
    url: https://github.com/dfguan/purge_dups/issues
  maturity: null
  name: purge_dups
  operatingSystem:
  - Mac
  - Linux
  otherID: []
  owner: Pub2Tools
  publication:
  - doi: 10.1101/729962
    metadata: null
    note: null
    pmcid: null
    pmid: null
    type: []
    version: null
  relation: []
  toolType: []
  topic:
  - term: Sequence assembly
    uri: http://edamontology.org/topic_0196
  validated: 1
  version:
  - v.1.2.6
- accessibility: null
  additionDate: '2016-09-30T07:30:11Z'
  biotoolsCURIE: biotools:silvangs
  biotoolsID: silvangs
  collectionID:
  - de.NBI
  - de.NBI-biodata
  - DSMZ Digital Diversity
  confidence_flag: null
  cost: Free of charge (with restrictions)
  credit:
  - email: ngs-contact@arb-silva.de
    fundrefid: null
    gridid: grid.507782.f
    name: SILVA Team
    note: null
    orcidid: null
    rorid: 027z9pz32
    typeEntity: Division
    typeRole:
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    url: https://www.arb-silva.de/contact/team/
  - email: hub@dsmz.de
    fundrefid: null
    gridid: grid.420081.f
    name: Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures
    note: null
    orcidid: null
    rorid: 02tyer376
    typeEntity: Institute
    typeRole:
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    url: https://www.dsmz.de
  description: SILVAngs is a data analysis service for ribosomal RNA gene (rDNA) amplicon
    reads from high-throughput sequencing (next-generation sequencing (NGS)) approaches
    based on an automatic software pipeline. It uses the SILVA rDNA databases, taxonomies,
    and alignments as a reference. It facilitates the classification of rDNA reads
    and provides a wealth of results (tables, graphs and sequence files) for download.
  documentation:
  - note: null
    type:
    - User manual
    url: https://www.arb-silva.de/fileadmin/silva_databases/sngs/SILVAngs_User_Guide.pdf
  - note: null
    type:
    - FAQ
    url: https://www.arb-silva.de/documentation/silvangs/userfaq/
  - note: null
    type:
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    url: https://www.arb-silva.de/footer/sngs-termsofuse
  download: []
  editPermission:
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  elixirNode:
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  elixirPlatform:
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  function:
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    input:
    - data:
        term: Nucleic acid sequence
        uri: http://edamontology.org/data_2977
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
    note: The pipeline accepts input data in Multi-Fasta format with each input file
      representing one sample. Samples that belong to one project (a transect, timeseries
      etc.) should be uploaded as a single SILVAngs project.
    operation:
    - term: Visualisation
      uri: http://edamontology.org/operation_0337
    - term: Statistical calculation
      uri: http://edamontology.org/operation_2238
    - term: Nucleic acid sequence analysis
      uri: http://edamontology.org/operation_2478
    - term: Taxonomic classification
      uri: http://edamontology.org/operation_3460
    - term: Validation
      uri: http://edamontology.org/operation_2428
    - term: Sequence clustering
      uri: http://edamontology.org/operation_0291
    - term: Sequence alignment
      uri: http://edamontology.org/operation_0292
    output:
    - data:
        term: Matrix
        uri: http://edamontology.org/data_2082
      format:
      - term: TSV
        uri: http://edamontology.org/format_3475
    - data:
        term: Plot
        uri: http://edamontology.org/data_2884
      format: []
    - data:
        term: Report
        uri: http://edamontology.org/data_2048
      format:
      - term: PDF
        uri: http://edamontology.org/format_3508
    - data:
        term: Sequence cluster (nucleic acid)
        uri: http://edamontology.org/data_1246
      format:
      - term: FASTA-aln
        uri: http://edamontology.org/format_1984
    - data:
        term: Nucleic acid sequence
        uri: http://edamontology.org/data_2977
      format:
      - term: ARB
        uri: http://edamontology.org/format_3830
      - term: FASTA-aln
        uri: http://edamontology.org/format_1984
  homepage: https://ngs.arb-silva.de
  homepage_status: 0
  language: []
  lastUpdate: '2025-06-30T13:26:39.251875Z'
  license: null
  link: []
  maturity: Mature
  name: SILVAngs
  operatingSystem: []
  otherID: []
  owner: silva
  publication:
  - doi: 10.1093/nar/gks1219
    metadata:
      abstract: SILVA (from Latin silva, forest, http://www.arb-silva.de) is a comprehensive
        web resource for up to date, quality-controlled databases of aligned ribosomal
        RNA (rRNA) gene sequences from the Bacteria, Archaea and Eukaryota domains
        and supplementary online services. The referred database release 111 (July
        2012) contains 3194 778 small subunit and 288717 large subunit rRNA gene sequences.
        Since the initial description of the project, substantial new features have
        been introduced, including advanced quality control procedures, an improved
        rRNA gene aligner, online tools for probe and primer evaluation and optimized
        browsing, searching and downloading on the website. Furthermore, the extensively
        curated SILVA taxonomy and the new non-redundant SILVA datasets provide an
        ideal reference for high-throughput classification of data from next-generation
        sequencing approaches. © The Author(s) 2012.
      authors:
      - name: Quast C.
      - name: Pruesse E.
      - name: Yilmaz P.
      - name: Gerken J.
      - name: Schweer T.
      - name: Yarza P.
      - name: Peplies J.
      - name: Glockner F.O.
      citationCount: 22633
      date: '2013-01-01T00:00:00Z'
      journal: Nucleic Acids Research
      title: 'The SILVA ribosomal RNA gene database project: Improved data processing
        and web-based tools'
    note: null
    pmcid: PMC3531112
    pmid: '23193283'
    type:
    - Primary
    version: null
  - doi: 10.1093/nar/gkt1209
    metadata:
      abstract: SILVA (from Latin silva, forest, http://www.arb-silva.de) is a comprehensive
        resource for up-to-date quality-controlled databases of aligned ribosomal
        RNA (rRNA) gene sequences from the Bacteria, Archaea and Eukaryota domains
        and supplementary online services. SILVA provides a manually curated taxonomy
        for all three domains of life, based on representative phylogenetic trees
        for the small- and large-subunit rRNA genes. This article describes the improvements
        the SILVA taxonomy has undergone in the last 3 years. Specifically we are
        focusing on the curation process, the various resources used for curation
        and the comparison of the SILVA taxonomy with Greengenes and RDP-II taxonomies.
        Our comparisons not only revealed a reasonable overlap between the taxa names,
        but also points to significant differences in both names and numbers of taxa
        between the three resources. © 2013 The Author(s). Published by Oxford University
        Press.
      authors:
      - name: Yilmaz P.
      - name: Parfrey L.W.
      - name: Yarza P.
      - name: Gerken J.
      - name: Pruesse E.
      - name: Quast C.
      - name: Schweer T.
      - name: Peplies J.
      - name: Ludwig W.
      - name: Glockner F.O.
      citationCount: 2590
      date: '2014-01-01T00:00:00Z'
      journal: Nucleic Acids Research
      title: The SILVA and "all-species Living Tree Project (LTP)" taxonomic frameworks
    note: null
    pmcid: PMC3965112
    pmid: '24293649'
    type:
    - Primary
    version: null
  - doi: 10.1093/bioinformatics/bts252
    metadata:
      abstract: 'Motivation: In the analysis of homologous sequences, computation
        of multiple sequence alignments (MSAs) has become a bottleneck. This is especially
        troublesome for marker genes like the ribosomal RNA (rRNA) where already millions
        of sequences are publicly available and individual studies can easily produce
        hundreds of thousands of new sequences. Methods have been developed to cope
        with such numbers, but further improvements are needed to meet accuracy requirements.Results:
        In this study, we present the SILVA Incremental Aligner (SINA) used to align
        the rRNA gene databases provided by the SILVA ribosomal RNA project. SINA
        uses a combination of k-mer searching and partial order alignment (POA) to
        maintain very high alignment accuracy while satisfying high throughput performance
        demands. SINA was evaluated in comparison with the commonly used high throughput
        MSA programs PyNAST and mothur. The three BRAliBase III benchmark MSAs could
        be reproduced with 99.3, 97.6 and 96.1 accuracy. A larger benchmark MSA comprising
        38 772 sequences could be reproduced with 98.9 and 99.3% accuracy using reference
        MSAs comprising 1000 and 5000 sequences. SINA was able to achieve higher accuracy
        than PyNAST and mothur in all performed benchmarks. © The Author(s) 2012.
        Published by Oxford University Press.'
      authors:
      - name: Pruesse E.
      - name: Peplies J.
      - name: Glockner F.O.
      citationCount: 2408
      date: '2012-07-01T00:00:00Z'
      journal: Bioinformatics
      title: 'SINA: Accurate high-throughput multiple sequence alignment of ribosomal
        RNA genes'
    note: null
    pmcid: PMC3389763
    pmid: '22556368'
    type:
    - Primary
    version: null
  relation:
  - biotoolsID: silva
    type: uses
  toolType:
  - Web application
  topic:
  - term: Metagenomics
    uri: http://edamontology.org/topic_3174
  - term: Biodiversity
    uri: http://edamontology.org/topic_3050
  - term: Taxonomy
    uri: http://edamontology.org/topic_0637
  - term: Functional, regulatory and non-coding RNA
    uri: http://edamontology.org/topic_0659
  - term: Sequence analysis
    uri: http://edamontology.org/topic_0080
  - term: Microbial ecology
    uri: http://edamontology.org/topic_3697
  validated: 1
  version:
  - 1.9.10
- accessibility: Open access
  additionDate: '2018-05-28T14:50:09Z'
  biotoolsCURIE: biotools:deepsig
  biotoolsID: deepsig
  collectionID:
  - Bologna Biocomputing Group
  confidence_flag: tool
  cost: Free of charge
  credit:
  - email: null
    fundrefid: null
    gridid: null
    name: ELIXIR-ITA-BOLOGNA
    note: null
    orcidid: null
    rorid: null
    typeEntity: Institute
    typeRole:
    - Provider
    url: http://biocomp.unibo.it
  - email: castrense.savojardo2@unibo.it
    fundrefid: null
    gridid: null
    name: Castrense Savojardo
    note: null
    orcidid: https://orcid.org/0000-0002-7359-0633
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    - Primary contact
    url: null
  - email: pierluigi.martelli@unibo.it
    fundrefid: null
    gridid: null
    name: Pier Luigi Martelli
    note: null
    orcidid: https://orcid.org/0000-0002-0274-5669
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: http://biocomp.unibo.it
  description: Prediction of secretory signal peptides in protein sequences
  documentation:
  - note: null
    type:
    - Command-line options
    url: https://github.com/BolognaBiocomp/deepsig
  download:
  - note: null
    type: Source code
    url: https://github.com/BolognaBiocomp/deepsig
    version: 1.2.5
  - note: null
    type: Container file
    url: https://hub.docker.com/r/bolognabiocomp/deepsig
    version: 1.2.5
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    type: group
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  elixirNode:
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  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input:
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        term: Protein sequence (raw)
        uri: http://edamontology.org/data_2974
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
    - data:
        term: Taxonomy
        uri: http://edamontology.org/data_3028
      format:
      - term: Textual format
        uri: http://edamontology.org/format_2330
    note: null
    operation:
    - term: Protein signal peptide detection
      uri: http://edamontology.org/operation_0418
    output:
    - data:
        term: Protein report
        uri: http://edamontology.org/data_0896
      format:
      - term: HTML
        uri: http://edamontology.org/format_2331
  homepage: https://busca.biocomp.unibo.it/deepsig/
  homepage_status: 0
  language:
  - Python
  - C++
  lastUpdate: '2025-06-19T11:55:09.017105Z'
  license: GPL-3.0
  link: []
  maturity: Mature
  name: DeepSig
  operatingSystem:
  - Linux
  - Windows
  - Mac
  otherID: []
  owner: ELIXIR-ITA-BOLOGNA
  publication:
  - doi: 10.1093/bioinformatics/btx818
    metadata:
      abstract: Motivation The identification of signal peptides in protein sequences
        is an important step toward protein localization and function characterization.
        Results Here, we present DeepSig, an improved approach for signal peptide
        detection and cleavage-site prediction based on deep learning methods. Comparative
        benchmarks performed on an updated independent dataset of proteins show that
        DeepSig is the current best performing method, scoring better than other available
        state-of-the-art approaches on both signal peptide detection and precise cleavage-site
        identification. Availability and implementation DeepSig is available as both
        standalone program and web server at https://deepsig.biocomp.unibo.it. All
        datasets used in this study can be obtained from the same website.
      authors:
      - name: Savojardo C.
      - name: Martelli P.L.
      - name: Fariselli P.
      - name: Casadio R.
      citationCount: 96
      date: '2018-05-15T00:00:00Z'
      journal: Bioinformatics
      title: 'DeepSig: Deep learning improves signal peptide detection in proteins'
    note: null
    pmcid: PMC5946842
    pmid: '29280997'
    type:
    - Primary
    version: '1.0'
  relation: []
  toolType:
  - Web application
  - Command-line tool
  topic:
  - term: Computational biology
    uri: http://edamontology.org/topic_3307
  - term: Protein sites, features and motifs
    uri: http://edamontology.org/topic_3510
  - term: Protein properties
    uri: http://edamontology.org/topic_0123
  validated: 1
  version:
  - 1.2.5
- accessibility: Open access
  additionDate: '2019-09-13T12:51:16Z'
  biotoolsCURIE: biotools:kraken2
  biotoolsID: kraken2
  collectionID:
  - ONTeater
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: null
    fundrefid: null
    gridid: null
    name: Derrick E. Wood
    note: null
    orcidid: http://orcid.org/0000-0002-7429-1854
    rorid: null
    typeEntity: Person
    typeRole: []
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Jennifer Lu
    note: null
    orcidid: http://orcid.org/0000-0001-9167-2002
    rorid: null
    typeEntity: Person
    typeRole: []
    url: null
  - email: langmea@cs.jhu.edu
    fundrefid: null
    gridid: null
    name: Ben Langmead
    note: null
    orcidid: http://orcid.org/0000-0003-2437-1976
    rorid: null
    typeEntity: Person
    typeRole: []
    url: null
  description: 'Kraken 2 is the newest version of Kraken, a taxonomic classification
    system using exact k-mer matches to achieve high accuracy and fast classification
    speeds. This classifier matches each k-mer within a query sequence to the lowest
    common ancestor (LCA) of all genomes containing the given k-mer. The k-mer assignments
    inform the classification algorithm.

    Any assumption that Kraken’s raw read assignments can be directly translated into
    species or strain-level abundance estimates is flawed. Bracken (Bayesian Reestimation
    of Abundance after Classification with KrakEN), estimates species abundances in
    metagenomics samples by probabilistically re-distributing reads in the taxonomic
    tree. (Lu, Jennifer et al. “Bracken: estimating species abundance in metagenomics
    data.”)'
  documentation:
  - note: null
    type:
    - User manual
    url: https://github.com/DerrickWood/kraken2/wiki/Manual
  - note: Links to multiple Kraken 2 and bracken databases and indexes
    type:
    - User manual
    url: https://benlangmead.github.io/aws-indexes/k2
  download:
  - note: null
    type: Source code
    url: https://github.com/DerrickWood/kraken2/archive/v2.0.8-beta.tar.gz
    version: 2.0.8-beta
  editPermission:
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    type: group
  elixirCommunity: []
  elixirNode: []
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  elixir_badge: 0
  function:
  - cmd: '`kraken2 --db <kraken2_database> <input.fastq>`'
    input:
    - data:
        term: DNA sequence
        uri: http://edamontology.org/data_3494
      format:
      - term: FASTQ
        uri: http://edamontology.org/format_1930
      - term: FASTA
        uri: http://edamontology.org/format_1929
    note: null
    operation:
    - term: Taxonomic classification
      uri: http://edamontology.org/operation_3460
    output:
    - data:
        term: Taxonomy
        uri: http://edamontology.org/data_3028
      format:
      - term: TSV
        uri: http://edamontology.org/format_3475
  homepage: https://ccb.jhu.edu/software/kraken2/
  homepage_status: 0
  language:
  - C++
  - Perl
  lastUpdate: '2025-06-18T12:24:26.657325Z'
  license: MIT
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/DerrickWood/kraken2
  - note: null
    type:
    - Issue tracker
    url: https://github.com/DerrickWood/kraken2/issues
  maturity: null
  name: kraken2
  operatingSystem: []
  otherID: []
  owner: anand-anshu
  publication:
  - doi: 10.1101/762302
    metadata: null
    note: null
    pmcid: null
    pmid: null
    type: []
    version: null
  relation:
  - biotoolsID: kraken
    type: isNewVersionOf
  - biotoolsID: bracken
    type: usedBy
  toolType:
  - Command-line tool
  topic:
  - term: Taxonomy
    uri: http://edamontology.org/topic_0637
  - term: Metagenomics
    uri: http://edamontology.org/topic_3174
  - term: Microbial ecology
    uri: http://edamontology.org/topic_3697
  - term: Microbiology
    uri: http://edamontology.org/topic_3301
  validated: 1
  version:
  - 2.0.8-beta
- accessibility: Open access
  additionDate: '2021-05-26T21:13:32Z'
  biotoolsCURIE: biotools:nextdenovo
  biotoolsID: nextdenovo
  collectionID:
  - ONTeater
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: support@nextomics.org
    fundrefid: null
    gridid: null
    name: Nextomics
    note: null
    orcidid: null
    rorid: null
    typeEntity: Institute
    typeRole:
    - Primary contact
    url: null
  description: NextDenovo is a string graph-based de novo assembler for long reads
    (CLR, HiFi and ONT). It uses a "correct-then-assemble" strategy similar to canu
    (no correction step for PacBio Hifi reads), but requires significantly less computing
    resources and storages.
  documentation:
  - note: null
    type:
    - User manual
    url: https://nextdenovo.readthedocs.io/en/latest/
  download:
  - note: null
    type: Source code
    url: https://github.com/Nextomics/NextDenovo/releases/tag/2.5.2
    version: null
  editPermission:
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  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Sequence trace
        uri: http://edamontology.org/data_0924
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
      - term: FASTQ
        uri: http://edamontology.org/format_1930
    note: null
    operation:
    - term: De-novo assembly
      uri: http://edamontology.org/operation_0524
    - term: Genome assembly
      uri: http://edamontology.org/operation_0525
    output:
    - data:
        term: Sequence assembly
        uri: http://edamontology.org/data_0925
      format:
      - term: Sequence assembly format (text)
        uri: http://edamontology.org/format_2561
      - term: FASTA
        uri: http://edamontology.org/format_1929
  homepage: https://github.com/Nextomics/NextDenovo
  homepage_status: 0
  language:
  - Python
  - C
  lastUpdate: '2025-06-18T12:20:23.607241Z'
  license: GPL-3.0
  link:
  - note: null
    type:
    - Issue tracker
    url: https://github.com/Nextomics/NextDenovo/issues
  maturity: Mature
  name: NextDenovo
  operatingSystem: []
  otherID: []
  owner: Kigaard
  publication:
  - doi: 10.1101/2023.03.09.531669.
    metadata: null
    note: null
    pmcid: null
    pmid: null
    type: []
    version: null
  relation: []
  toolType:
  - Command-line tool
  topic:
  - term: Sequencing
    uri: http://edamontology.org/topic_3168
  - term: Sequence assembly
    uri: http://edamontology.org/topic_0196
  validated: 0
  version:
  - v.2.5.2
- accessibility: Open access
  additionDate: '2021-05-27T09:04:45Z'
  biotoolsCURIE: biotools:quickmerge
  biotoolsID: quickmerge
  collectionID:
  - ONTeater
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: null
    fundrefid: null
    gridid: null
    name: Mahul Chakraborty
    note: null
    orcidid: https://orcid.org/0000-0003-2414-9187
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: https://mahulchakraborty.wordpress.com/
  description: Quickmerge is a program that uses complementary information from genomes
    assembled with long reads in order to improve contiguity, and works with assemblies
    derived from both Pacific Biosciences or Oxford Nanopore. Quickmerge will even
    work with hybrid assemblies made by combining long reads and Illumina short reads.
  documentation: []
  download: []
  editPermission:
    authors:
    - ELIXIR-CZ
    - Keiler_Collier
    type: group
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: merge_wrapper.py -pre output_prefix assembly_1.fa assembly_2.fa
    input:
    - data:
        term: Sequence set (nucleic acid)
        uri: http://edamontology.org/data_1234
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
    note: 'Runs whole merge process on an input assembly.

      Assembly 2 will be used to fill gaps in assembly 1.'
    operation:
    - term: Genome assembly
      uri: http://edamontology.org/operation_0525
    - term: Scaffolding
      uri: http://edamontology.org/operation_3216
    - term: De-novo assembly
      uri: http://edamontology.org/operation_0524
    - term: Genotyping
      uri: http://edamontology.org/operation_3196
    output:
    - data:
        term: Sequence set (nucleic acid)
        uri: http://edamontology.org/data_1234
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
  homepage: https://github.com/mahulchak/quickmerge
  homepage_status: 0
  language:
  - C++
  - C
  lastUpdate: '2025-06-18T12:17:20.983962Z'
  license: GPL-3.0
  link:
  - note: null
    type:
    - Issue tracker
    url: https://github.com/mahulchak/quickmerge/issues
  - note: null
    type:
    - Repository
    url: https://github.com/mahulchak/quickmerge
  maturity: null
  name: quickmerge
  operatingSystem:
  - Mac
  - Linux
  otherID: []
  owner: Kigaard
  publication:
  - doi: 10.1534/g3.118.200162
    metadata:
      abstract: Accurate and comprehensive characterization of genetic variation is
        essential for deciphering the genetic basis of diseases and other phenotypes.
        A vast amount of genetic variation stems from largescale sequence changes
        arising from the duplication, deletion, inversion, and translocation of sequences.
        In the past 10 years, high-throughput short reads have greatly expanded our
        ability to assay sequence variation due to single nucleotide polymorphisms.
        However, a recent de novo assembly of a second Drosophila melanogaster reference
        genome has revealed that short read genotyping methods miss hundreds of structural
        variants, including those affecting phenotypes. While genomes assembled using
        highcoverage long reads can achieve high levels of contiguity and completeness,
        concerns about cost, errors, and low yield have limited widespread adoption
        of such sequencing approaches. Here we resequenced the reference strain of
        D. melanogaster (ISO1) on a single Oxford Nanopore MinION flow cell run for
        24 hr. Using only reads longer than 1 kb or with at least 30x coverage, we
        assembled a highly contiguous de novo genome. The addition of inexpensive
        paired reads and subsequent scaffolding using an optical map technology achieved
        an assembly with completeness and contiguity comparable to the D. melanogaster
        reference assembly. Comparison of our assembly to the reference assembly of
        ISO1 uncovered a number of structural variants (SVs), including novel LTR
        transposable element insertions and duplications affecting genes with developmental,
        behavioral, and metabolic functions. Collectively, these SVs provide a snapshot
        of the dynamics of genome evolution. Furthermore, our assembly and comparison
        to the D. melanogaster reference genome demonstrates that high-quality de
        novo assembly of reference genomes and comprehensive variant discovery using
        such assemblies are now possible by a single lab for under $1,000 (USD).
      authors:
      - name: Solares E.A.
      - name: Chakraborty M.
      - name: Miller D.E.
      - name: Kalsow S.
      - name: Hall K.
      - name: Perera A.G.
      - name: Emerson J.J.
      - name: Scott Hawley R.
      citationCount: 70
      date: '2018-10-01T00:00:00Z'
      journal: 'G3: Genes, Genomes, Genetics'
      title: Rapid low-cost assembly of the drosophila melanogaster reference genome
        using low-coverage, long-read sequencing
    note: null
    pmcid: PMC6169397
    pmid: '30018084'
    type:
    - Primary
    version: null
  relation: []
  toolType:
  - Command-line tool
  topic:
  - term: Structural variation
    uri: http://edamontology.org/topic_3175
  - term: Sequence assembly
    uri: http://edamontology.org/topic_0196
  - term: DNA polymorphism
    uri: http://edamontology.org/topic_2885
  - term: Whole genome sequencing
    uri: http://edamontology.org/topic_3673
  - term: Genotype and phenotype
    uri: http://edamontology.org/topic_0625
  validated: 0
  version:
  - v.0.3
- accessibility: Open access
  additionDate: '2017-01-13T13:16:01Z'
  biotoolsCURIE: biotools:quast
  biotoolsID: quast
  collectionID:
  - ONTeater
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: quast.support@cab.spbu.ru
    fundrefid: null
    gridid: null
    name: QUAST Support
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: null
  description: "QUAST stands for QUality ASsessment Tool.  \nIt evaluates a quality\
    \ of genome assemblies by computing various metrics and providing nice reports."
  documentation:
  - note: null
    type:
    - General
    url: http://quast.bioinf.spbau.ru/
  download: []
  editPermission:
    authors:
    - ELIXIR-CZ
    - Keiler_Collier
    type: group
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: quast -ek assembly.fa --out output_prefix
    input:
    - data:
        term: Sequence set (nucleic acid)
        uri: http://edamontology.org/data_1234
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
    note: '# Running quast on a eukaryotic genome'
    operation:
    - term: Visualisation
      uri: http://edamontology.org/operation_0337
    - term: Sequence assembly validation
      uri: http://edamontology.org/operation_3180
    output: []
  homepage: http://quast.sourceforge.net/quast
  homepage_status: 0
  language:
  - Perl
  - Python
  - C
  lastUpdate: '2025-06-18T11:53:52.861712Z'
  license: GPL-2.0
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/ablab/quast
  - note: null
    type:
    - Issue tracker
    url: https://github.com/ablab/quast/issues
  maturity: Mature
  name: QUAST
  operatingSystem:
  - Linux
  - Mac
  otherID: []
  owner: seqwiki_import
  publication:
  - doi: 10.1093/bioinformatics/btt086
    metadata:
      abstract: Limitations of genome sequencing techniques have led to dozens of
        assembly algorithms, none of which is perfect. A number of methods for comparing
        assemblers have been developed, but none is yet a recognized benchmark. Further,
        most existing methods for comparing assemblies are only applicable to new
        assemblies of finished genomes; the problem of evaluating assemblies of previously
        unsequenced species has not been adequately considered. Here, we present QUAST
        - a quality assessment tool for evaluating and comparing genome assemblies.
        This tool improves on leading assembly comparison software with new ideas
        and quality metrics. QUAST can evaluate assemblies both with a reference genome,
        as well as without a reference. QUAST produces many reports, summary tables
        and plots to help scientists in their research and in their publications.
        In this study, we used QUAST to compare several genome assemblers on three
        datasets. QUAST tables and plots for all of them are available in the Supplementary
        Material, and interactive versions of these reports are on the QUAST website.
        © 2013 The Author.
      authors:
      - name: Gurevich A.
      - name: Saveliev V.
      - name: Vyahhi N.
      - name: Tesler G.
      citationCount: 6872
      date: '2013-04-15T00:00:00Z'
      journal: Bioinformatics
      title: 'QUAST: Quality assessment tool for genome assemblies'
    note: null
    pmcid: PMC3624806
    pmid: '23422339'
    type: []
    version: null
  relation: []
  toolType:
  - Workflow
  topic:
  - term: Sequence assembly
    uri: http://edamontology.org/topic_0196
  validated: 1
  version:
  - v.5.3.0
- accessibility: Open access
  additionDate: '2019-11-14T18:44:38Z'
  biotoolsCURIE: biotools:Racon
  biotoolsID: Racon
  collectionID:
  - ONTeater
  confidence_flag: tool
  cost: Free of charge
  credit:
  - email: cskang@korea.kr
    fundrefid: null
    gridid: null
    name: Chon-Sik Kang
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole: []
    url: null
  - email: changsookim@cnu.ac.kr
    fundrefid: null
    gridid: null
    name: Changsoo Kim
    note: null
    orcidid: https://orcid.org/0000-0002-3596-2934
    rorid: null
    typeEntity: Person
    typeRole: []
    url: null
  description: 'Consensus module for raw de novo DNA assembly of long uncorrected
    reads


    Racon is intended as a standalone consensus module to correct raw contigs generated
    by rapid assembly methods which do not include a consensus step. The goal of Racon
    is to generate genomic consensus which is of similar or better quality compared
    to the output generated by assembly methods which employ both error correction
    and consensus steps, while providing a speedup of several times compared to those
    methods. It supports data produced by both Pacific Biosciences and Oxford Nanopore
    Technologies.'
  documentation: []
  download: []
  editPermission:
    authors: []
    type: public
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: racon -u reads.fa mapped_reads.sam assembly.fa > assembly_racon.fa
    input:
    - data:
        term: Nucleic acid sequence alignment
        uri: http://edamontology.org/data_1383
      format:
      - term: BAM
        uri: http://edamontology.org/format_2572
      - term: SAM
        uri: http://edamontology.org/format_2573
    - data:
        term: Sequence set (nucleic acid)
        uri: http://edamontology.org/data_1234
      format:
      - term: FASTQ
        uri: http://edamontology.org/format_1930
    - data:
        term: Sequence set (nucleic acid)
        uri: http://edamontology.org/data_1234
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
    note: '# The mapping file can be generated with any mapping program - eg, bwa-mem
      or minimap2.

      # The following is an example using minimap2 with ONT data

      minimap2 assembly.fa-ax map-ont reads.fa > mapped_reads.sam'
    operation:
    - term: Genome assembly
      uri: http://edamontology.org/operation_0525
    - term: Mapping assembly
      uri: http://edamontology.org/operation_0523
    output:
    - data:
        term: Sequence set (nucleic acid)
        uri: http://edamontology.org/data_1234
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
  homepage: https://github.com/isovic/racon
  homepage_status: 0
  language:
  - C++
  - Python
  lastUpdate: '2025-06-18T11:42:42.378216Z'
  license: MIT
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/isovic/racon
  - note: null
    type:
    - Issue tracker
    url: https://github.com/isovic/racon/issues
  maturity: null
  name: Racon
  operatingSystem:
  - Mac
  - Linux
  otherID: []
  owner: Pub2Tools
  publication:
  - doi: 10.3390/plants8080270
    metadata:
      abstract: 'The whole genome sequencing (WGS) has become a crucial tool in understanding
        genome structure and genetic variation. The MinION sequencing of Oxford Nanopore
        Technologies (ONT) is an excellent approach for performing WGS and it has
        advantages in comparison with other Next-Generation Sequencing (NGS): It is
        relatively inexpensive, portable, has simple library preparation, can be monitored
        in real-time, and has no theoretical limits on reading length. Sorghum bicolor
        (L.) Moench is diploid (2n = 2x = 20) with a genome size of about 730 Mb,
        and its genome sequence information is released in the Phytozome database.
        Therefore, sorghum can be used as a good reference. However, plant species
        have complex and large genomes when compared to animals or microorganisms.
        As a result, complete genome sequencing is difficult for plant species. MinION
        sequencing that produces long-reads can be an excellent tool for overcoming
        the weak assembly of short-reads generated from NGS by minimizing the generation
        of gaps or covering the repetitive sequence that appears on the plant genome.
        Here, we conducted the genome sequencing for S. bicolor cv. BTx623 while using
        the MinION platform and obtained 895,678 reads and 17.9 gigabytes (Gb) (ca.
        25× coverage of reference) from long-read sequence data. A total of 6124 contigs
        (covering 45.9%) were generated from Canu, and a total of 2661 contigs (covering
        50%) were generated from Minimap and Miniasm with a Racon through a de novo
        assembly using two different tools and mapped assembled contigs against the
        sorghum reference genome. Our results provide an optimal series of long-read
        sequencing analysis for plant species while using the MinION platform and
        a clue to determine the total sequencing scale for optimal coverage that is
        based on various genome sizes.'
      authors:
      - name: Lee Y.G.
      - name: Choi S.C.
      - name: Kang Y.
      - name: Kim K.M.
      - name: Kang C.-S.
      - name: Kim C.
      citationCount: 13
      date: '2019-08-01T00:00:00Z'
      journal: Plants
      title: 'Constructing a reference genome in a single lab: The possibility to
        use oxford nanopore technology'
    note: null
    pmcid: PMC6724115
    pmid: '31390788'
    type: []
    version: null
  relation: []
  toolType: []
  topic:
  - term: Whole genome sequencing
    uri: http://edamontology.org/topic_3673
  - term: Sequence assembly
    uri: http://edamontology.org/topic_0196
  validated: 1
  version: []
- accessibility: null
  additionDate: '2016-10-10T07:21:30Z'
  biotoolsCURIE: biotools:busco
  biotoolsID: busco
  collectionID: []
  confidence_flag: null
  cost: null
  credit:
  - email: null
    fundrefid: null
    gridid: null
    name: SIB Swiss Institute of Bioinformatics
    note: null
    orcidid: null
    rorid: null
    typeEntity: Institute
    typeRole:
    - Provider
    url: null
  - email: evgeny.zdobnov@unige.ch
    fundrefid: null
    gridid: null
    name: null
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: null
  description: Provides measures for quantitative assessment of genome assembly, gene
    set, and transcriptome completeness based on evolutionarily informed expectations
    of gene content from near-universal single-copy orthologs.
  documentation:
  - note: null
    type:
    - User manual
    url: https://busco.ezlab.org/busco_userguide.html
  download: []
  editPermission:
    authors: []
    type: public
  elixirCommunity: []
  elixirNode:
  - Switzerland
  elixirPlatform:
  - Tools
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Sequence set (nucleic acid)
        uri: http://edamontology.org/data_1234
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
    note: null
    operation:
    - term: Sequence assembly validation
      uri: http://edamontology.org/operation_3180
    output:
    - data:
        term: Sequence report
        uri: http://edamontology.org/data_2955
      format: []
  homepage: https://busco.ezlab.org/
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2025-06-17T15:10:57.224896Z'
  license: null
  link: []
  maturity: null
  name: BUSCO
  operatingSystem:
  - Linux
  otherID: []
  owner: SIB
  publication:
  - doi: 10.1093/bioinformatics/btv351
    metadata:
      abstract: 'Motivation: Genomics has revolutionized biological research, but
        quality assessment of the resulting assembled sequences is complicated and
        remains mostly limited to technical measures like N50. Results: We propose
        a measure for quantitative assessment of genome assembly and annotation completeness
        based on evolutionarily informed expectations of gene content. We implemented
        the assessment procedure in open-source software, with sets of Benchmarking
        Universal Single-Copy Orthologs, named BUSCO.'
      authors:
      - name: Simao F.A.
      - name: Waterhouse R.M.
      - name: Ioannidis P.
      - name: Kriventseva E.V.
      - name: Zdobnov E.M.
      citationCount: 8766
      date: '2015-10-01T00:00:00Z'
      journal: Bioinformatics
      title: 'BUSCO: Assessing genome assembly and annotation completeness with single-copy
        orthologs'
    note: null
    pmcid: null
    pmid: '26059717'
    type: []
    version: null
  - doi: 10.1002/cpz1.323
    metadata:
      abstract: 'Evaluation of the quality of genomic “data products” such as genome
        assemblies or gene sets is of critical importance in order to recognize possible
        issues and correct them during the generation of new data. It is equally essential
        to guide subsequent or comparative analyses with existing data, as the correct
        interpretation of the results necessarily requires knowledge about the quality
        level and reliability of the inputs. Using datasets of near universal single-copy
        orthologs derived from OrthoDB, BUSCO can estimate the completeness and redundancy
        of genomic data by providing biologically meaningful metrics based on expected
        gene content. These can complement technical metrics such as contiguity measures
        (e.g., number of contigs/scaffolds, and N50 values). Here, we describe the
        use of the BUSCO tool suite to assess different data types that can range
        from genome assemblies of single isolates and assembled transcriptomes and
        annotated gene sets to metagenome-assembled genomes where the taxonomic origin
        of the species is unknown. BUSCO is the only tool capable of assessing all
        these types of sequences from both eukaryotic and prokaryotic species. The
        protocols detail the various BUSCO running modes and the novel workflows introduced
        in versions 4 and 5, including the batch analysis on multiple inputs, the
        auto-lineage workflow to run assessments without specifying a dataset, and
        a workflow for the evaluation of (large) eukaryotic genomes. The protocols
        further cover the BUSCO setup, guidelines to interpret the results, and BUSCO
        “plugin” workflows for performing common operations in genomics using BUSCO
        results, such as building phylogenomic trees and visualizing syntenies. ©
        2021 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic
        Protocol 1: Assessing an input sequence with a BUSCO dataset specified manually.
        Basic Protocol 2: Assessing an input sequence with a dataset automatically
        selected by BUSCO. Basic Protocol 3: Assessing multiple inputs. Alternate
        Protocol: Decreasing analysis runtime when assessing a large number of small
        genomes with BUSCO auto-lineage workflow and Snakemake. Support Protocol 1:
        BUSCO setup. Support Protocol 2: Visualizing BUSCO results. Support Protocol
        3: Building phylogenomic trees.'
      authors:
      - name: Manni M.
      - name: Berkeley M.R.
      - name: Seppey M.
      - name: Zdobnov E.M.
      citationCount: 566
      date: '2021-12-01T00:00:00Z'
      journal: Current Protocols
      title: 'BUSCO: Assessing Genomic Data Quality and Beyond'
    note: null
    pmcid: null
    pmid: '34936221'
    type: []
    version: null
  - doi: 10.1093/molbev/msx319
    metadata:
      abstract: Genomics promises comprehensive surveying of genomes and metagenomes,
        but rapidly changing technologies and expanding data volumes make evaluation
        of completeness a challenging task. Technical sequencing quality metrics can
        be complemented by quantifying completeness of genomic data sets in terms
        of the expected gene content of Benchmarking Universal Single-Copy Orthologs
        (BUSCO, http://busco.ezlab.org). The latest software release implements a
        complete refactoring of the code tomake itmore flexible and extendable to
        facilitate high-Throughput assessments. The original six lineage assessment
        data sets have been updated with improved species sampling, 34 new subsets
        have been built for vertebrates, arthropods, fungi, and prokaryotes that greatly
        enhance resolution, and data sets are now also available for nematodes, protists,
        and plants. Here, we present BUSCO v3 with example analyses that highlight
        the wideranging utility of BUSCO assessments, which extend beyond quality
        control of genomics data sets to applications in comparative genomics analyses,
        gene predictor training, metagenomics, and phylogenomics.
      authors:
      - name: Waterhouse R.M.
      - name: Seppey M.
      - name: Simao F.A.
      - name: Manni M.
      - name: Ioannidis P.
      - name: Klioutchnikov G.
      - name: Kriventseva E.V.
      - name: Zdobnov E.M.
      citationCount: 1508
      date: '2018-03-01T00:00:00Z'
      journal: Molecular Biology and Evolution
      title: BUSCO applications from quality assessments to gene prediction and phylogenomics
    note: null
    pmcid: PMC5850278
    pmid: '29220515'
    type: []
    version: null
  - doi: 10.1093/molbev/msab199
    metadata:
      abstract: Methods for evaluating the quality of genomic and metagenomic data
        are essential to aid genome assembly procedures and to correctly interpret
        the results of subsequent analyses. BUSCO estimates the completeness and redundancy
        of processed genomic data based on universal single-copy orthologs. Here,
        we present new functionalities and major improvements of the BUSCO software,
        as well as the renewal and expansion of the underlying data sets in sync with
        the OrthoDB v10 release. Among the major novelties, BUSCO now enables phylogenetic
        placement of the input sequence to automatically select the most appropriate
        BUSCO data set for the assessment, allowing the analysis of metagenome-Assembled
        genomes of unknown origin. A newly introduced genome workflow increases the
        efficiency and runtimes especially on large eukaryotic genomes. BUSCO is the
        only tool capable of assessing both eukaryotic and prokaryotic species, and
        can be applied to various data types, from genome assemblies and metagenomic
        bins, to transcriptomes and gene sets.
      authors:
      - name: Manni M.
      - name: Berkeley M.R.
      - name: Seppey M.
      - name: Simao F.A.
      - name: Zdobnov E.M.
      citationCount: 2710
      date: '2021-10-01T00:00:00Z'
      journal: Molecular Biology and Evolution
      title: 'BUSCO Update: Novel and Streamlined Workflows along with Broader and
        Deeper Phylogenetic Coverage for Scoring of Eukaryotic, Prokaryotic, and Viral
        Genomes'
    note: null
    pmcid: PMC8476166
    pmid: '34320186'
    type: []
    version: null
  relation: []
  toolType:
  - Command-line tool
  topic:
  - term: Sequence assembly
    uri: http://edamontology.org/topic_0196
  - term: Genomics
    uri: http://edamontology.org/topic_0622
  - term: Transcriptomics
    uri: http://edamontology.org/topic_3308
  - term: Sequence analysis
    uri: http://edamontology.org/topic_0080
  validated: 1
  version:
  - '1'
- accessibility: Open access
  additionDate: '2017-08-20T16:07:58Z'
  biotoolsCURIE: biotools:htslib
  biotoolsID: htslib
  collectionID:
  - Animal and Crop Genomics
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    note: null
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    rorid: null
    typeEntity: Institute
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    typeEntity: Project
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  description: The main purpose of HTSlib is to provide access to genomic information
    files, both alignment data (SAM, BAM, and CRAM formats) and variant data (VCF
    and BCF formats). The library also provides interfaces to access and index genome
    reference data in FASTA format and tab-delimited files with genomic coordinates.
    It is utilized and incorporated into both SAMtools and BCFtools.
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  - note: null
    type:
    - User manual
    url: http://www.htslib.org/doc/#manual-pages
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      - term: BAM
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      - term: CRAM
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      - term: FASTA
        uri: http://edamontology.org/format_1929
      - term: FASTQ
        uri: http://edamontology.org/format_1930
    - data:
        term: Sequence variations
        uri: http://edamontology.org/data_3498
      format:
      - term: VCF
        uri: http://edamontology.org/format_3016
      - term: BCF
        uri: http://edamontology.org/format_3020
    note: null
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    - term: Data handling
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      - term: BAM
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      - term: CRAM
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      - term: FASTQ
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    - data:
        term: Sequence variations
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      format:
      - term: VCF
        uri: http://edamontology.org/format_3016
      - term: BCF
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  - C
  lastUpdate: '2025-06-03T09:00:20.313887Z'
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  - note: null
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  - note: null
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    - Mailing list
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    - Issue tracker
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    metadata:
      abstract: 'Background: Since the original publication of the VCF and SAM formats,
        an explosion of software tools have been created to process these data files.
        To facilitate this a library was produced out of the original SAMtools implementation,
        with a focus on performance and robustness. The file formats themselves have
        become international standards under the jurisdiction of the Global Alliance
        for Genomics and Health. Findings: We present a software library for providing
        programmatic access to sequencing alignment and variant formats. It was born
        out of the widely used SAMtools and BCFtools applications. Considerable improvements
        have been made to the original code plus many new features including newer
        access protocols, the addition of the CRAM file format, better indexing and
        iterators, and better use of threading. Conclusion: Since the original Samtools
        release, performance has been considerably improved, with a BAM read-write
        loop running 5 times faster and BAM to SAM conversion 13 times faster (both
        using 16 threads, compared to Samtools 0.1.19). Widespread adoption has seen
        HTSlib downloaded >1 million times from GitHub and conda. The C library has
        been used directly by an estimated 900 GitHub projects and has been incorporated
        into Perl, Python, Rust, and R, significantly expanding the number of uses
        via other languages. HTSlib is open source and is freely available from htslib.org
        under MIT/BSD license.'
      authors:
      - name: Bonfield J.K.
      - name: Marshall J.
      - name: Danecek P.
      - name: Li H.
      - name: Ohan V.
      - name: Whitwham A.
      - name: Keane T.
      citationCount: 189
      date: '2021-02-01T00:00:00Z'
      journal: GigaScience
      title: 'HTSlib: C library for reading/writing high-Throughput sequencing data'
    note: 'HTSlib: C library for reading/writing high-throughput sequencing data.'
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    pmid: '33594436'
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    - Primary
    version: null
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  - '1.1'
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    note: null
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    note: null
    operation:
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    note: null
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    - term: Nucleic acid sequence analysis
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  - cmd: null
    input:
    - data:
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    note: null
    operation:
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      format: []
  - cmd: null
    input:
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      format:
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    note: null
    operation:
    - term: Nucleosome position prediction
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    - term: Phasing
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  homepage: https://www.multiscalegenomics.eu/
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  language:
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  - Python
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  license: Apache-2.0
  link:
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    - Service
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    type:
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    type:
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  topic:
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  - term: ChIP-seq
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  - term: Nucleic acid structure analysis
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  additionDate: '2016-05-17T10:18:56Z'
  biotoolsCURIE: biotools:splicemachine
  biotoolsID: splicemachine
  collectionID:
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  description: Splice site prediction.
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    type:
    - General
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  additionDate: '2015-06-29T10:15:39Z'
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  description: Neural network predictions of splice sites in human, C. elegans and
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    note: Neural network predictions of splice sites
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  publication:
  - doi: 10.1093/nar/24.17.3439
    metadata:
      abstract: Artificial neural networks have been combined with a rule based system
        to predict intron splice sites in the dicot plant Arabidopsis thaliana. A
        two step prediction scheme, where a global prediction of the coding potential
        regulates a cutoff level for a local prediction of splice sites, is refined
        by rules based on splice site confidence values, prediction scores, coding
        context and distances between potential splice sites. In this approach, the
        prediction of splice sites mutually affect each other in a non-local manner.
        The combined approach drastically reduces the large amount of false positive
        splice sites normally haunting splice site prediction. An analysis of the
        errors made by the networks in the first step of the method revealed a previously
        unknown feature, a frequent T-tract prolongation containing cryptic acceptor
        sites in the 5' end of exons. The method presented here has been compared
        with three other approaches, GeneFinder, GeneMark and Grail. Overall the method
        presented here is an order of magnitude better. We show that the new method
        is able to find a donor site in the coding sequence for the jelly fish Green
        Fluorescent Protein, exactly at the position that was experimentally observed
        in A.thaliana transformants. Predictions for alternatively spliced genes are
        also presented, together with examples of genes from other dicots, monocots
        and algae. The method has been made available through electronic mail.
      authors:
      - name: Hebsgaard S.M.
      - name: Korning P.G.
      - name: Tolstrup N.
      - name: Engelbrecht J.
      - name: Rouze P.
      - name: Brunak S.
      citationCount: 690
      date: '1996-01-01T00:00:00Z'
      journal: Nucleic Acids Research
      title: Splice site prediction in Arabidopsis thaliana pre-mRNA by combining
        local and global sequence information
    note: null
    pmcid: PMC146109
    pmid: '8811101'
    type:
    - Other
    version: null
  - doi: 10.1093/nar/24.17.3439
    metadata:
      abstract: Artificial neural networks have been combined with a rule based system
        to predict intron splice sites in the dicot plant Arabidopsis thaliana. A
        two step prediction scheme, where a global prediction of the coding potential
        regulates a cutoff level for a local prediction of splice sites, is refined
        by rules based on splice site confidence values, prediction scores, coding
        context and distances between potential splice sites. In this approach, the
        prediction of splice sites mutually affect each other in a non-local manner.
        The combined approach drastically reduces the large amount of false positive
        splice sites normally haunting splice site prediction. An analysis of the
        errors made by the networks in the first step of the method revealed a previously
        unknown feature, a frequent T-tract prolongation containing cryptic acceptor
        sites in the 5' end of exons. The method presented here has been compared
        with three other approaches, GeneFinder, GeneMark and Grail. Overall the method
        presented here is an order of magnitude better. We show that the new method
        is able to find a donor site in the coding sequence for the jelly fish Green
        Fluorescent Protein, exactly at the position that was experimentally observed
        in A.thaliana transformants. Predictions for alternatively spliced genes are
        also presented, together with examples of genes from other dicots, monocots
        and algae. The method has been made available through electronic mail.
      authors:
      - name: Hebsgaard S.M.
      - name: Korning P.G.
      - name: Tolstrup N.
      - name: Engelbrecht J.
      - name: Rouze P.
      - name: Brunak S.
      citationCount: 690
      date: '1996-01-01T00:00:00Z'
      journal: Nucleic Acids Research
      title: Splice site prediction in Arabidopsis thaliana pre-mRNA by combining
        local and global sequence information
    note: null
    pmcid: PMC146109
    pmid: '8811101'
    type:
    - Other
    version: null
  relation: []
  toolType:
  - Command-line tool
  - Web application
  topic:
  - term: Sequence sites, features and motifs
    uri: http://edamontology.org/topic_0160
  - term: Gene transcripts
    uri: http://edamontology.org/topic_3512
  validated: 1
  version:
  - '1.0'
- accessibility: null
  additionDate: '2016-01-19T16:39:56Z'
  biotoolsCURIE: biotools:openms
  biotoolsID: openms
  collectionID:
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    note: null
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    name: Eberhard-Karls-Universität Tübingen
    note: null
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    rorid: null
    typeEntity: Institute
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    url: null
  - email: null
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    name: Freie Universität Berlin
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    url: null
  - email: open-ms-general@lists.sourceforge.net
    fundrefid: null
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    note: null
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    rorid: null
    typeEntity: null
    typeRole:
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    url: null
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    typeEntity: Person
    typeRole:
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    url: null
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    fundrefid: null
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    name: Hannes Röst
    note: null
    orcidid: http://orcid.org/0000-0003-0990-7488
    rorid: null
    typeEntity: Person
    typeRole:
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  description: Open source library and a collection of tools and interfaces for the
    analysis of mass spectrometry data. Includes over 200 standalone (TOPP) tools
    that can be combined to a workflow with the integrated workflow editor TOPPAS.
    Raw and intermediate mass spectrometry data can be visualised with the included
    viewer TOPPView.
  documentation:
  - note: null
    type:
    - General
    url: http://ftp.mi.fu-berlin.de/pub/OpenMS/release-documentation/html/index.html
  download:
  - note: null
    type: Source code
    url: https://github.com/OpenMS/OpenMS
    version: null
  - note: null
    type: Binaries
    url: http://sourceforge.net/projects/open-ms/files/OpenMS/OpenMS-2.0/
    version: null
  - note: null
    type: Source code
    url: https://github.com/OpenMS/OpenMS
    version: null
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        term: Mass spectrometry data
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      format:
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      - term: mzQuantML
        uri: http://edamontology.org/format_3248
      - term: dta
        uri: http://edamontology.org/format_3652
      - term: FASTA
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      - term: protXML
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      - term: idXML
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      - term: OBO
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      - term: XML
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      - term: TraML
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      - term: mzML
        uri: http://edamontology.org/format_3244
      - term: mzIdentML
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      - term: mzXML
        uri: http://edamontology.org/format_3654
      - term: MGF
        uri: http://edamontology.org/format_3651
      - term: qcML
        uri: http://edamontology.org/format_3683
    - data:
        term: Sequence record
        uri: http://edamontology.org/data_0849
      format:
      - term: pepXML
        uri: http://edamontology.org/format_3655
      - term: mzQuantML
        uri: http://edamontology.org/format_3248
      - term: dta
        uri: http://edamontology.org/format_3652
      - term: FASTA
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      - term: protXML
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      - term: idXML
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      - term: OBO
        uri: http://edamontology.org/format_2549
      - term: XML
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      - term: TraML
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      - term: mzML
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      - term: mzIdentML
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      - term: mzXML
        uri: http://edamontology.org/format_3654
      - term: MGF
        uri: http://edamontology.org/format_3651
      - term: qcML
        uri: http://edamontology.org/format_3683
    - data:
        term: Peptide identification
        uri: http://edamontology.org/data_0945
      format:
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        uri: http://edamontology.org/format_3655
      - term: mzQuantML
        uri: http://edamontology.org/format_3248
      - term: dta
        uri: http://edamontology.org/format_3652
      - term: FASTA
        uri: http://edamontology.org/format_1929
      - term: protXML
        uri: http://edamontology.org/format_3747
      - term: idXML
        uri: http://edamontology.org/format_3764
      - term: OBO
        uri: http://edamontology.org/format_2549
      - term: XML
        uri: http://edamontology.org/format_2332
      - term: TraML
        uri: http://edamontology.org/format_3246
      - term: mzML
        uri: http://edamontology.org/format_3244
      - term: mzIdentML
        uri: http://edamontology.org/format_3247
      - term: mzXML
        uri: http://edamontology.org/format_3654
      - term: MGF
        uri: http://edamontology.org/format_3651
      - term: qcML
        uri: http://edamontology.org/format_3683
    note: null
    operation:
    - term: Protein identification
      uri: http://edamontology.org/operation_3767
    - term: Parsing
      uri: http://edamontology.org/operation_1812
    - term: Data handling
      uri: http://edamontology.org/operation_2409
    - term: Chromatographic alignment
      uri: http://edamontology.org/operation_3628
    - term: Mass spectra calibration
      uri: http://edamontology.org/operation_3627
    - term: Formatting
      uri: http://edamontology.org/operation_0335
    - term: Protein quantification
      uri: http://edamontology.org/operation_3630
    - term: Retention time prediction
      uri: http://edamontology.org/operation_3633
    - term: Annotation
      uri: http://edamontology.org/operation_0226
    - term: Protein feature detection
      uri: http://edamontology.org/operation_3092
    - term: Isotope-coded protein label
      uri: http://edamontology.org/operation_3705
    - term: Label-free quantification
      uri: http://edamontology.org/operation_3634
    - term: iTRAQ
      uri: http://edamontology.org/operation_3639
    - term: Peptide identification
      uri: http://edamontology.org/operation_3631
    - term: Peak detection
      uri: http://edamontology.org/operation_3215
    - term: Mass spectrum visualisation
      uri: http://edamontology.org/operation_3694
    - term: Labeled quantification
      uri: http://edamontology.org/operation_3635
    - term: Splitting
      uri: http://edamontology.org/operation_3359
    - term: Spectral analysis
      uri: http://edamontology.org/operation_3214
    - term: Deisotoping
      uri: http://edamontology.org/operation_3629
    - term: Target-Decoy
      uri: http://edamontology.org/operation_3649
    - term: Prediction and recognition (protein)
      uri: http://edamontology.org/operation_3023
    - term: Comparison
      uri: http://edamontology.org/operation_2424
    - term: Standardisation and normalisation
      uri: http://edamontology.org/operation_3435
    output:
    - data:
        term: Peptide identification
        uri: http://edamontology.org/data_0945
      format:
      - term: pepXML
        uri: http://edamontology.org/format_3655
      - term: mzQuantML
        uri: http://edamontology.org/format_3248
      - term: dta
        uri: http://edamontology.org/format_3652
      - term: FASTA
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      - term: idXML
        uri: http://edamontology.org/format_3764
      - term: mzXML
        uri: http://edamontology.org/format_3654
      - term: TraML
        uri: http://edamontology.org/format_3246
      - term: mzML
        uri: http://edamontology.org/format_3244
      - term: mzIdentML
        uri: http://edamontology.org/format_3247
      - term: MGF
        uri: http://edamontology.org/format_3651
      - term: qcML
        uri: http://edamontology.org/format_3683
    - data:
        term: Expression data
        uri: http://edamontology.org/data_2603
      format:
      - term: pepXML
        uri: http://edamontology.org/format_3655
      - term: mzQuantML
        uri: http://edamontology.org/format_3248
      - term: dta
        uri: http://edamontology.org/format_3652
      - term: FASTA
        uri: http://edamontology.org/format_1929
      - term: idXML
        uri: http://edamontology.org/format_3764
      - term: mzXML
        uri: http://edamontology.org/format_3654
      - term: TraML
        uri: http://edamontology.org/format_3246
      - term: mzML
        uri: http://edamontology.org/format_3244
      - term: mzIdentML
        uri: http://edamontology.org/format_3247
      - term: MGF
        uri: http://edamontology.org/format_3651
      - term: qcML
        uri: http://edamontology.org/format_3683
  homepage: http://www.openms.de
  homepage_status: 0
  language:
  - C++
  lastUpdate: '2025-04-30T11:39:30.251890Z'
  license: BSD-3-Clause
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/OpenMS/OpenMS
  maturity: Mature
  name: OpenMS
  operatingSystem:
  - Linux
  - Windows
  - Mac
  otherID: []
  owner: samwein
  publication:
  - doi: 10.1038/nmeth.3959
    metadata:
      abstract: © 2016 Nature America, Inc. All rights reserved.High-resolution mass
        spectrometry (MS) has become an important tool in the life sciences, contributing
        to the diagnosis and understanding of human diseases, elucidating biomolecular
        structural information and characterizing cellular signaling networks. However,
        the rapid growth in the volume and complexity of MS data makes transparent,
        accurate and reproducible analysis difficult. We present OpenMS 2.0 (http://www.openms.de),
        a robust, open-source, cross-platform software specifically designed for the
        flexible and reproducible analysis of high-throughput MS data. The extensible
        OpenMS software implements common mass spectrometric data processing tasks
        through a well-defined application programming interface in C++ and Python
        and through standardized open data formats. OpenMS additionally provides a
        set of 185 tools and ready-made workflows for common mass spectrometric data
        processing tasks, which enable users to perform complex quantitative mass
        spectrometric analyses with ease.
      authors:
      - name: Rost H.L.
      - name: Sachsenberg T.
      - name: Aiche S.
      - name: Bielow C.
      - name: Weisser H.
      - name: Aicheler F.
      - name: Andreotti S.
      - name: Ehrlich H.-C.
      - name: Gutenbrunner P.
      - name: Kenar E.
      - name: Liang X.
      - name: Nahnsen S.
      - name: Nilse L.
      - name: Pfeuffer J.
      - name: Rosenberger G.
      - name: Rurik M.
      - name: Schmitt U.
      - name: Veit J.
      - name: Walzer M.
      - name: Wojnar D.
      - name: Wolski W.E.
      - name: Schilling O.
      - name: Choudhary J.S.
      - name: Malmstrom L.
      - name: Aebersold R.
      - name: Reinert K.
      - name: Kohlbacher O.
      citationCount: 246
      date: '2016-08-30T00:00:00Z'
      journal: Nature Methods
      title: 'OpenMS: A flexible open-source software platform for mass spectrometry
        data analysis'
    note: null
    pmcid: null
    pmid: '27575624'
    type:
    - Primary
    version: null
  - doi: 10.1007/978-1-60761-987-1_23
    metadata:
      abstract: Proteomics experiments based on state-of-the-art mass spectrometry
        produce vast amounts of data, which cannot be analyzed manually. Hence, software
        is needed which is able to analyze the data in an automated fashion. The need
        for robust and reusable software tools triggered the development of libraries
        implementing different algorithms for the various analysis steps. OpenMS is
        such a software library and provides a wealth of data structures and algorithms
        for the analysis of mass spectrometric data. For users unfamiliar with programming,
        TOPP ("The OpenMS Proteomics Pipeline") offers a wide range of already implemented
        tools sharing the same interface and designed for a specific analysis task
        each. TOPP thus makes the sophisticated algorithms of OpenMS accessible to
        nonprogrammers. The individual TOPP tools can be strung together into pipelines
        for analyzing mass spectrometry-based experiments starting from the raw output
        of the mass spectrometer. These analysis pipelines can be constructed using
        a graphical editor. Even complex analytical workflows can thus be analyzed
        with ease.
      authors:
      - name: Bertsch A.
      - name: Gropl C.
      - name: Reinert K.
      - name: Kohlbacher O.
      citationCount: 65
      date: '2011-01-01T00:00:00Z'
      journal: Methods in molecular biology (Clifton, N.J.)
      title: 'OpenMS and TOPP: open source software for LC-MS data analysis.'
    note: null
    pmcid: null
    pmid: null
    type:
    - Other
    version: null
  relation: []
  toolType:
  - Library
  - Workbench
  topic:
  - term: Proteomics experiment
    uri: http://edamontology.org/topic_3520
  - term: Proteomics
    uri: http://edamontology.org/topic_0121
  - term: Metabolomics
    uri: http://edamontology.org/topic_3172
  validated: 1
  version:
  - 2.0.0
- accessibility: null
  additionDate: '2017-08-20T15:57:59Z'
  biotoolsCURIE: biotools:metaphlan
  biotoolsID: metaphlan
  collectionID:
  - Animal and Crop Genomics
  confidence_flag: null
  cost: null
  credit:
  - email: null
    fundrefid: null
    gridid: null
    name: null
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: https://groups.google.com/forum/#!forum/metaphlan-users
  description: Computational tool for profiling the composition of microbial communities
    from metagenomic shotgun sequencing data.
  documentation:
  - note: null
    type:
    - General
    url: https://github.com/biobakery/MetaPhlAn
  download: []
  editPermission:
    authors:
    - animalandcropgenomics
    - ELIXIR-CZ
    - bebatut
    - vashokan
    type: group
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: metaphlan <fastq_input> --input_type fastq -o <output>
    input:
    - data:
        term: DNA sequence
        uri: http://edamontology.org/data_3494
      format:
      - term: FASTQ
        uri: http://edamontology.org/format_1930
      - term: FASTA
        uri: http://edamontology.org/format_1929
      - term: SAM
        uri: http://edamontology.org/format_2573
    note: null
    operation:
    - term: Taxonomic classification
      uri: http://edamontology.org/operation_3460
    output:
    - data:
        term: Taxonomy
        uri: http://edamontology.org/data_3028
      format:
      - term: DSV
        uri: http://edamontology.org/format_3751
  - cmd: sgb_to_gtdb_profile.py -i <metaphlan_output> -o <gtdb_metaphlan_output>
    input:
    - data:
        term: Taxonomy
        uri: http://edamontology.org/data_3028
      format:
      - term: DSV
        uri: http://edamontology.org/format_3751
    note: Convert SGB-based profile to GTDB taxonomy
    operation:
    - term: Taxonomic classification
      uri: http://edamontology.org/operation_3460
    output:
    - data:
        term: Taxonomy
        uri: http://edamontology.org/data_3028
      format:
      - term: DSV
        uri: http://edamontology.org/format_3751
  homepage: http://segatalab.cibio.unitn.it/tools/metaphlan/index.html
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2025-04-22T12:44:24.859435Z'
  license: MIT
  link: []
  maturity: null
  name: MetaPhlAn
  operatingSystem:
  - Linux
  - Windows
  - Mac
  otherID: []
  owner: admin
  publication:
  - doi: 10.1038/nmeth.2066
    metadata:
      abstract: Metagenomic shotgun sequencing data can identify microbes populating
        a microbial community and their proportions, but existing taxonomic profiling
        methods are inefficient for increasingly large data sets. We present an approach
        that uses clade-specific marker genes to unambiguously assign reads to microbial
        clades more accurately and >50Ã-faster than current approaches. We validated
        our metagenomic phylogenetic analysis tool, MetaPhlAn, on terabases of short
        reads and provide the largest metagenomic profiling to date of the human gut.
        It can be accessed at http://huttenhower.sph.harvard.edu/ metaphlan/. © 2012
        Nature America, Inc. All rights reserved.
      authors:
      - name: Segata N.
      - name: Waldron L.
      - name: Ballarini A.
      - name: Narasimhan V.
      - name: Jousson O.
      - name: Huttenhower C.
      citationCount: 1300
      date: '2012-08-01T00:00:00Z'
      journal: Nature Methods
      title: Metagenomic microbial community profiling using unique clade-specific
        marker genes
    note: null
    pmcid: PMC3443552
    pmid: '22688413'
    type:
    - Primary
    version: null
  relation: []
  toolType:
  - Command-line tool
  topic:
  - term: Metagenomics
    uri: http://edamontology.org/topic_3174
  - term: Phylogenomics
    uri: http://edamontology.org/topic_0194
  validated: 1
  version: []
- accessibility: null
  additionDate: '2015-06-29T10:14:28Z'
  biotoolsCURIE: biotools:netpicorna
  biotoolsID: netpicorna
  collectionID: []
  confidence_flag: null
  cost: Free of charge (with restrictions)
  credit:
  - email: null
    fundrefid: null
    gridid: null
    name: CBS
    note: null
    orcidid: null
    rorid: null
    typeEntity: Institute
    typeRole:
    - Provider
    url: null
  - email: nikob@cbs.dtu.dk
    fundrefid: null
    gridid: null
    name: Nikolaj Sorgenfrei Blom
    note: null
    orcidid: https://orcid.org/0000-0001-7787-7853
    rorid: null
    typeEntity: Person
    typeRole: []
    url: null
  description: Neural network predictions of cleavage sites of picornaviral proteases.
  documentation:
  - note: null
    type:
    - General
    url: http://www.cbs.dtu.dk/services/NetPicoRNA/instructions.php
  download: []
  editPermission:
    authors:
    - powehi
    type: group
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Sequence
        uri: http://edamontology.org/data_2044
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
    note: produces neural network predictions of cleavage sites of picornaviral proteases
    operation:
    - term: Protein cleavage site prediction
      uri: http://edamontology.org/operation_0422
    output:
    - data:
        term: Protein features
        uri: http://edamontology.org/data_1277
      format:
      - term: Textual format
        uri: http://edamontology.org/format_2330
    - data:
        term: Sequence report
        uri: http://edamontology.org/data_2955
      format:
      - term: Binary format
        uri: http://edamontology.org/format_2333
  homepage: http://cbs.dtu.dk/services/NetPicoRNA/
  homepage_status: 0
  language: []
  lastUpdate: '2025-04-21T12:49:56.070719Z'
  license: Other
  link:
  - note: null
    type:
    - Software catalogue
    url: http://cbs.dtu.dk/services
  maturity: Legacy
  name: NetPicoRNA
  operatingSystem:
  - Linux
  otherID: []
  owner: powehi
  publication:
  - doi: 10.1002/pro.5560051107
    metadata:
      abstract: Picornaviral proteinases are responsible for maturation cleavages
        of the viral polyprotein, but also catalyze the degradation of cellular targets.
        Using graphical visualization techniques and neural network algorithms, we
        have investigated the sequence specificity of the two proteinases 2A(pro)
        and 3C(pro). The cleavage of VP0 (giving rise to VP2 and VP4), which is carried
        out by a so-far unknown proteinase, was also examined. In combination with
        a novel surface exposure prediction algorithm, our neural network approach
        successfully distinguishes known cleavage sites from noncleavage sites and
        yields a more consistent definition of features common to these sites. The
        method is able to predict experimentally determined cleavage sites in cellular
        proteins. We present a list of mammalian and other proteins that are predicted
        to be possible targets for the vital proteinases. Whether these proteins are
        indeed cleaved awaits experimental verification. Additionally, we report several
        errors detected in the protein databases.
      authors:
      - name: Blom N.
      - name: Hansen J.
      - name: Blaas D.
      - name: Brunak S.
      citationCount: 204
      date: '1996-01-01T00:00:00Z'
      journal: Protein Science
      title: 'Cleavage site analysis in picornaviral polyproteins: Discovering cellular
        targets by neural networks'
    note: null
    pmcid: PMC2143287
    pmid: '8931139'
    type:
    - Primary
    version: null
  relation: []
  toolType:
  - Web application
  topic:
  - term: Protein sites, features and motifs
    uri: http://edamontology.org/topic_3510
  - term: Sequence sites, features and motifs
    uri: http://edamontology.org/topic_0160
  validated: 1
  version:
  - '1.0'
- accessibility: Open access
  additionDate: '2025-02-28T15:04:33.594183Z'
  biotoolsCURIE: biotools:prolfquapp
  biotoolsID: prolfquapp
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit: []
  description: A command-line tool for differential expression analysis in quantitative
    proteomics
  documentation:
  - note: null
    type:
    - General
    url: https://github.com/prolfqua/prolfquapp/blob/master/README.md
  download:
  - note: null
    type: Downloads page
    url: https://github.com/prolfqua/prolfquapp/releases/tag/0.1.6
    version: 0.1.6
  editPermission:
    authors:
    - thatmariia
    type: group
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: './prolfqua_dea.sh -i data_dir/ -d annotation.xlsx -y config.yaml -w NameOfAnalysis
      -s DIANN

      # and again you run the version within the docker container with

      # ./prolfquapp_docker.sh prolfqua_dea.sh -i data_dir/ -d annotation.xlsx -y
      config.yaml -w NameOfAnalysis -s DIANN'
    input:
    - data:
        term: Expression data
        uri: http://edamontology.org/data_2603
      format:
      - term: CSV
        uri: http://edamontology.org/format_3752
      - term: TSV
        uri: http://edamontology.org/format_3475
    - data:
        term: Sequence
        uri: http://edamontology.org/data_2044
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
    note: null
    operation:
    - term: Differential protein expression profiling
      uri: http://edamontology.org/operation_3741
    output:
    - data:
        term: Expression data
        uri: http://edamontology.org/data_2603
      format:
      - term: xlsx
        uri: http://edamontology.org/format_3620
      - term: HTML
        uri: http://edamontology.org/format_2331
  - cmd: null
    input:
    - data:
        term: Expression data
        uri: http://edamontology.org/data_2603
      format:
      - term: xlsx
        uri: http://edamontology.org/format_3620
    note: null
    operation:
    - term: Validation
      uri: http://edamontology.org/operation_2428
    output:
    - data:
        term: Quality control report
        uri: http://edamontology.org/data_3914
      format:
      - term: HTML
        uri: http://edamontology.org/format_2331
  - cmd: null
    input:
    - data:
        term: Expression data
        uri: http://edamontology.org/data_2603
      format:
      - term: CSV
        uri: http://edamontology.org/format_3752
      - term: TSV
        uri: http://edamontology.org/format_3475
    - data:
        term: Protein sequence
        uri: http://edamontology.org/data_2976
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
    note: null
    operation:
    - term: Expression data visualisation
      uri: http://edamontology.org/operation_0571
    output:
    - data:
        term: Expression data
        uri: http://edamontology.org/data_2603
      format:
      - term: PDF
        uri: http://edamontology.org/format_3508
      - term: HTML
        uri: http://edamontology.org/format_2331
  homepage: https://github.com/prolfqua/prolfquapp
  homepage_status: 0
  language:
  - R
  lastUpdate: '2025-03-28T10:18:25.715685Z'
  license: MIT
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/prolfqua/prolfquapp
  - note: null
    type:
    - Issue tracker
    url: https://github.com/prolfqua/prolfquapp/issues
  maturity: Emerging
  name: prolfquapp
  operatingSystem:
  - Mac
  - Linux
  otherID: []
  owner: n.m.palmblad@lumc.nl
  publication:
  - doi: 10.1021/acs.jproteome.4c00911
    metadata:
      abstract: Mass spectrometry is a cornerstone of quantitative proteomics, enabling
        relative protein quantification and differential expression analysis (DEA)
        of proteins. As experiments grow in complexity, involving more samples, groups,
        and identified proteins, interactive differential expression analysis tools
        become impractical. The prolfquapp addresses this challenge by providing a
        command-line interface that simplifies DEA, making it accessible to nonprogrammers
        and seamlessly integrating it into workflow management systems. Prolfquapp
        streamlines data processing and result visualization by generating dynamic
        HTML reports that facilitate the exploration of differential expression results.
        These reports allow for investigating complex experiments, such as those involving
        repeated measurements or multiple explanatory variables. Additionally, prolfquapp
        supports various output formats, including XLSX files, SummarizedExperiment
        objects and rank files, for further interactive analysis using spreadsheet
        software, the exploreDE Shiny application, or gene set enrichment analysis
        software, respectively. By leveraging advanced statistical models from the
        prolfqua R package, prolfquapp offers a user-friendly, integrated solution
        for large-scale quantitative proteomics studies, combining efficient data
        processing with insightful, publication-ready outputs.
      authors:
      - name: Wolski W.E.
      - name: Grossmann J.
      - name: Schwarz L.
      - name: Leary P.
      - name: Turker C.
      - name: Nanni P.
      - name: Schlapbach R.
      - name: Panse C.
      citationCount: 0
      date: '2025-02-07T00:00:00Z'
      journal: Journal of Proteome Research
      title: prolfquapp ─ A User-Friendly Command-Line Tool Simplifying Differential
        Expression Analysis in Quantitative Proteomics
    note: null
    pmcid: null
    pmid: null
    type: []
    version: 0.0.6
  relation: []
  toolType:
  - Command-line tool
  topic:
  - term: Proteomics
    uri: http://edamontology.org/topic_0121
  validated: 0
  version:
  - 0.1.6
- accessibility: Open access
  additionDate: '2025-01-31T17:19:47.094256Z'
  biotoolsCURIE: biotools:proteomaker
  biotoolsID: proteomaker
  collectionID:
  - Proteomics
  confidence_flag: null
  cost: Free of charge
  credit: []
  description: ProteoMaker is a platform for the generation of an in-silico bottom-up
    proteomics data set with a ground truth on the level of proteoforms.
  documentation: []
  download:
  - note: null
    type: Source code
    url: https://github.com/computproteomics/ProteoMaker
    version: null
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Protein sequence
        uri: http://edamontology.org/data_2976
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
    note: null
    operation:
    - term: Simulated gene expression data generation
      uri: http://edamontology.org/operation_3566
    - term: Statistical calculation
      uri: http://edamontology.org/operation_2238
    output:
    - data:
        term: Gene expression matrix
        uri: http://edamontology.org/data_3112
      format:
      - term: CSV
        uri: http://edamontology.org/format_3752
    - data:
        term: Proteolytic digest
        uri: http://edamontology.org/data_1238
      format:
      - term: CSV
        uri: http://edamontology.org/format_3752
    - data:
        term: Quality control report
        uri: http://edamontology.org/data_3914
      format:
      - term: YAML
        uri: http://edamontology.org/format_3750
    - data:
        term: Statistical estimate score
        uri: http://edamontology.org/data_0951
      format:
      - term: CSV
        uri: http://edamontology.org/format_3752
  homepage: https://github.com/computproteomics/ProteoMaker
  homepage_status: 0
  language:
  - R
  lastUpdate: '2025-01-31T17:19:47.096981Z'
  license: MIT
  link:
  - note: Web application
    type:
    - Service
    url: https://computproteomics.bmb.sdu.dk/app_direct/ProteoMaker
  maturity: Mature
  name: ProteoMaker
  operatingSystem:
  - Mac
  - Linux
  - Windows
  otherID: []
  owner: veitveit11
  publication: []
  relation: []
  toolType:
  - Library
  - Web application
  topic:
  - term: Proteomics
    uri: http://edamontology.org/topic_0121
  - term: Proteomics experiment
    uri: http://edamontology.org/topic_3520
  - term: Simulation experiment
    uri: http://edamontology.org/topic_3524
  validated: 0
  version: []
- accessibility: Open access
  additionDate: '2023-08-30T13:03:57.407598Z'
  biotoolsCURIE: biotools:shic
  biotoolsID: shic
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: magnus.palmblad@gmail.com
    fundrefid: null
    gridid: null
    name: Magnus Palmblad
    note: null
    orcidid: https://orcid.org/0000-0002-5865-8994
    rorid: null
    typeEntity: null
    typeRole:
    - Primary contact
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Veit Schwämmle
    note: null
    orcidid: https://orcid.org/0000-0002-9708-6722
    rorid: null
    typeEntity: null
    typeRole: []
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Dirk Winkelhardt
    note: null
    orcidid: https://orcid.org/0000-0001-8770-2221
    rorid: null
    typeEntity: null
    typeRole: []
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Vedran Kasalica
    note: null
    orcidid: https://orcid.org/0000-0002-0097-1056
    rorid: null
    typeEntity: null
    typeRole: []
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Anna-Lena Lamprecht
    note: null
    orcidid: https://orcid.org/0000-0003-1953-5606
    rorid: null
    typeEntity: null
    typeRole: []
    url: null
  description: shic is a collection of shims for use in automated workflow composition
  documentation:
  - note: null
    type:
    - General
    url: https://github.com/magnuspalmblad/shic/README.md
  download: []
  editPermission:
    authors:
    - VKasalica
    - veits@bmb.sdu.dk
    type: group
  elixirCommunity:
  - Proteomics
  - Galaxy
  - Metabolomics
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Protein report
        uri: http://edamontology.org/data_0896
      format:
      - term: protXML
        uri: http://edamontology.org/format_3747
    note: null
    operation:
    - term: Conversion
      uri: http://edamontology.org/operation_3434
    output:
    - data:
        term: ID list
        uri: http://edamontology.org/data_2872
      format:
      - term: TSV
        uri: http://edamontology.org/format_3475
  - cmd: null
    input:
    - data:
        term: Mass spectrometry data
        uri: http://edamontology.org/data_2536
      format:
      - term: MGF
        uri: http://edamontology.org/format_3651
    note: null
    operation:
    - term: Conversion
      uri: http://edamontology.org/operation_3434
    output:
    - data:
        term: Mass spectrometry data
        uri: http://edamontology.org/data_2536
      format:
      - term: MGF
        uri: http://edamontology.org/format_3651
  - cmd: null
    input:
    - data:
        term: Sequence distance matrix
        uri: http://edamontology.org/data_0870
      format:
      - term: Nexus format
        uri: http://edamontology.org/format_1912
    note: null
    operation:
    - term: Conversion
      uri: http://edamontology.org/operation_3434
    output:
    - data:
        term: Sequence distance matrix
        uri: http://edamontology.org/data_0870
      format:
      - term: mega
        uri: http://edamontology.org/format_1991
  - cmd: null
    input:
    - data:
        term: Protein sequence
        uri: http://edamontology.org/data_2976
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
    note: null
    operation:
    - term: Conversion
      uri: http://edamontology.org/operation_3434
    output:
    - data:
        term: UniProt accession
        uri: http://edamontology.org/data_3021
      format:
      - term: TSV
        uri: http://edamontology.org/format_3475
  - cmd: null
    input:
    - data:
        term: Peptide identification
        uri: http://edamontology.org/data_0945
      format:
      - term: pepXML
        uri: http://edamontology.org/format_3655
    note: null
    operation:
    - term: Conversion
      uri: http://edamontology.org/operation_3434
    output:
    - data:
        term: Protein sequence
        uri: http://edamontology.org/data_2976
      format:
      - term: TSV
        uri: http://edamontology.org/format_3475
  - cmd: null
    input:
    - data:
        term: Peptide identification
        uri: http://edamontology.org/data_0945
      format:
      - term: mzIdentML
        uri: http://edamontology.org/format_3247
    note: null
    operation:
    - term: Conversion
      uri: http://edamontology.org/operation_3434
    output:
    - data:
        term: Protein sequence
        uri: http://edamontology.org/data_2976
      format:
      - term: TSV
        uri: http://edamontology.org/format_3475
  - cmd: null
    input:
    - data:
        term: Text mining report
        uri: http://edamontology.org/data_0972
      format:
      - term: XML
        uri: http://edamontology.org/format_2332
    note: null
    operation:
    - term: Conversion
      uri: http://edamontology.org/operation_3434
    output:
    - data:
        term: ChEBI ID
        uri: http://edamontology.org/data_1174
      format:
      - term: TSV
        uri: http://edamontology.org/format_3475
  - cmd: null
    input:
    - data:
        term: Peptide identification
        uri: http://edamontology.org/data_0945
      format:
      - term: TSV
        uri: http://edamontology.org/format_3475
    note: null
    operation:
    - term: Conversion
      uri: http://edamontology.org/operation_3434
    output:
    - data:
        term: Peptide identification
        uri: http://edamontology.org/data_0945
      format:
      - term: mzIdentML
        uri: http://edamontology.org/format_3247
  - cmd: null
    input:
    - data:
        term: Protein report
        uri: http://edamontology.org/data_0896
      format:
      - term: TSV
        uri: http://edamontology.org/format_3475
    note: null
    operation:
    - term: Conversion
      uri: http://edamontology.org/operation_3434
    output:
    - data:
        term: ID list
        uri: http://edamontology.org/data_2872
      format:
      - term: TSV
        uri: http://edamontology.org/format_3475
  - cmd: null
    input:
    - data:
        term: Peptide identification
        uri: http://edamontology.org/data_0945
      format:
      - term: pepXML
        uri: http://edamontology.org/format_3655
    note: null
    operation:
    - term: Conversion
      uri: http://edamontology.org/operation_3434
    output:
    - data:
        term: Protein name
        uri: http://edamontology.org/data_1009
      format:
      - term: Textual format
        uri: http://edamontology.org/format_2330
  - cmd: null
    input:
    - data:
        term: Peptide identification
        uri: http://edamontology.org/data_0945
      format:
      - term: pepXML
        uri: http://edamontology.org/format_3655
    note: null
    operation:
    - term: Conversion
      uri: http://edamontology.org/operation_3434
    output:
    - data:
        term: Protein name (UniProt)
        uri: http://edamontology.org/data_2764
      format:
      - term: Textual format
        uri: http://edamontology.org/format_2330
  homepage: https://github.com/magnuspalmblad/shic
  homepage_status: 0
  language: []
  lastUpdate: '2025-01-16T16:39:33.218764Z'
  license: MIT
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/magnuspalmblad/shic
  maturity: null
  name: shic
  operatingSystem: []
  otherID: []
  owner: n.m.palmblad@lumc.nl
  publication: []
  relation: []
  toolType:
  - Script
  topic: []
  validated: 0
  version: []
- accessibility: Open access
  additionDate: '2024-05-05T10:53:14.688391Z'
  biotoolsCURIE: biotools:phiembed
  biotoolsID: phiembed
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: gonzales.markedward@gmail.com
    fundrefid: null
    gridid: null
    name: Mark Edward M. Gonzales
    note: Research Assistant, Bioinformatics Lab, Advanced Research Institute for
      Informatics, Computing and Networking, De La Salle University, Manila, Philippines
    orcidid: https://orcid.org/0000-0001-5050-3157
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    url: https://github.com/memgonzales
  - email: jennifer.ureta@gmail.com
    fundrefid: null
    gridid: null
    name: Jennifer C. Ureta
    note: Faculty, Bioinformatics Lab, Advanced Research Institute for Informatics,
      Computing and Networking, De La Salle University, Manila, Philippines
    orcidid: https://orcid.org/0000-0003-0427-5311
    rorid: null
    typeEntity: Person
    typeRole:
    - Contributor
    url: https://scholar.google.com/citations?user=v0Tf_u4AAAAJ&hl=en
  - email: anish.shrestha@dlsu.edu.ph
    fundrefid: null
    gridid: null
    name: Anish M.S. Shrestha
    note: Head, Bioinformatics Lab, Advanced Research Institute for Informatics, Computing
      and Networking, De La Salle University, Manila, Philippines
    orcidid: https://orcid.org/0000-0002-9192-9709
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: https://a-transposable-element.com/
  description: PHIEmbed is a phage-host interaction prediction tool that uses protein
    language models to represent the receptor-binding proteins of phages. It presents
    improvements over using handcrafted (manually feature-engineered) sequence properties
    and eliminates the need to manually extract and select features from phage sequences.
  documentation:
  - note: null
    type:
    - Installation instructions
    - Quick start guide
    - Citation instructions
    - Command-line options
    url: https://github.com/bioinfodlsu/phage-host-prediction
  download:
  - note: null
    type: Source code
    url: https://github.com/bioinfodlsu/phage-host-prediction
    version: null
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Protein sequence
        uri: http://edamontology.org/data_2976
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
    note: Predicts the host genus of a phage given its receptor-binding protein sequences
    operation:
    - term: Prediction and recognition
      uri: http://edamontology.org/operation_2423
    output:
    - data:
        term: Report
        uri: http://edamontology.org/data_2048
      format:
      - term: CSV
        uri: http://edamontology.org/format_3752
  homepage: https://github.com/bioinfodlsu/phage-host-prediction
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2025-01-14T09:13:55.932761Z'
  license: MIT
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/bioinfodlsu/phage-host-prediction
  - note: null
    type:
    - Service
    url: http://phiembed.bioinfodlsu.com/
  maturity: Emerging
  name: PHIEmbed
  operatingSystem:
  - Mac
  - Linux
  - Windows
  otherID: []
  owner: memgonzales
  publication:
  - doi: 10.1371/journal.pone.0289030
    metadata:
      abstract: With the growing interest in using phages to combat antimicrobial
        resistance, computational methods for predicting phage-host interactions have
        been explored to help shortlist candidate phages. Most existing models consider
        entire proteomes and rely on manual feature engineering, which poses difficulty
        in selecting the most informative sequence properties to serve as input to
        the model. In this paper, we framed phage-host interaction prediction as a
        multiclass classification problem that takes as input the embeddings of a
        phage’s receptor-binding proteins, which are known to be the key machinery
        for host recognition, and predicts the host genus. We explored different protein
        language models to automatically encode these protein sequences into dense
        embeddings without the need for additional alignment or structural information.
        We show that the use of embeddings of receptor-binding proteins presents improvements
        over handcrafted genomic and protein sequence features. The highest performance
        was obtained using the transformer-based protein language model ProtT5, resulting
        in a 3% to 4% increase in weighted F1 and recall scores across different prediction
        confidence thresholds, compared to using selected handcrafted sequence features.
      authors:
      - name: Gonzales M.E.M.
      - name: Ureta J.C.
      - name: Shrestha A.M.S.
      citationCount: 2
      date: '2023-07-01T00:00:00Z'
      journal: PLoS ONE
      title: Protein embeddings improve phage-host interaction prediction
    note: null
    pmcid: null
    pmid: '37486915'
    type:
    - Primary
    version: null
  relation: []
  toolType:
  - Command-line tool
  topic:
  - term: Machine learning
    uri: http://edamontology.org/topic_3474
  - term: Sequence analysis
    uri: http://edamontology.org/topic_0080
  - term: Proteins
    uri: http://edamontology.org/topic_0078
  - term: Proteomics
    uri: http://edamontology.org/topic_0121
  - term: Computational biology
    uri: http://edamontology.org/topic_3307
  - term: Bioinformatics
    uri: http://edamontology.org/topic_0091
  - term: Virology
    uri: http://edamontology.org/topic_0781
  validated: 0
  version: []
- accessibility: null
  additionDate: '2016-05-31T11:29:42Z'
  biotoolsCURIE: biotools:dynamine
  biotoolsID: dynamine
  collectionID: []
  confidence_flag: null
  cost: null
  credit:
  - email: null
    fundrefid: null
    gridid: null
    name: vub.ac.be
    note: null
    orcidid: null
    rorid: null
    typeEntity: Institute
    typeRole:
    - Provider
    url: null
  - email: wvranken@vub.ac.be
    fundrefid: null
    gridid: null
    name: Wim Vranken
    note: null
    orcidid: null
    rorid: null
    typeEntity: null
    typeRole:
    - Support
    url: null
  - email: wvranken@vub.ac.be
    fundrefid: null
    gridid: null
    name: Wim Vranken
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: null
  description: Protein backbone dynamics prediction from sequence.
  documentation:
  - note: null
    type:
    - General
    url: http://dynamine.ibsquare.be/help/
  download: []
  editPermission:
    authors:
    - tanish
    type: group
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Protein sequence (raw)
        uri: http://edamontology.org/data_2974
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
    note: Protein backbone dynamics prediction from sequence File containing one value
      per amino acid in each protein sequence
    operation:
    - term: Prediction and recognition
      uri: http://edamontology.org/operation_2423
    output:
    - data:
        term: Protein features
        uri: http://edamontology.org/data_1277
      format: []
  homepage: http://dynamine.ibsquare.be/
  homepage_status: 0
  language: []
  lastUpdate: '2025-01-08T15:03:40.105084Z'
  license: null
  link: []
  maturity: null
  name: DynaMine
  operatingSystem:
  - Linux
  - Windows
  - Mac
  otherID: []
  owner: wvranken@vub.ac.be
  publication:
  - doi: 10.1038/ncomms3741
    metadata: null
    note: null
    pmcid: null
    pmid: '24225580'
    type:
    - Other
    version: null
  - doi: 10.1093/nar/gku270
    metadata: null
    note: null
    pmcid: PMC4086073
    pmid: '24728994'
    type:
    - Other
    version: null
  relation: []
  toolType:
  - Web API
  - Web application
  topic:
  - term: Biophysics
    uri: http://edamontology.org/topic_3306
  - term: Protein properties
    uri: http://edamontology.org/topic_0123
  - term: Protein disordered structure
    uri: http://edamontology.org/topic_3538
  validated: 1
  version:
  - '1'
- accessibility: null
  additionDate: '2020-11-09T21:38:53Z'
  biotoolsCURIE: biotools:trend_protein_evolution_function
  biotoolsID: trend_protein_evolution_function
  collectionID: []
  confidence_flag: null
  cost: null
  credit:
  - email: gumerov.1@osu.edu
    fundrefid: null
    gridid: null
    name: Vadim Gumerov
    note: null
    orcidid: https://orcid.org/0000-0003-1670-7679
    rorid: null
    typeEntity: null
    typeRole: []
    url: null
  description: TREND is a platform that allows researchers to explore protein function
    and evolution identifying protein features, gene neighborhoods and operons, clustering
    neighboring genes, and integrating all these data into phylogenomic context and
    cross-referencing with RefSeq, Pfam, CDD and MiST databases. The platform provides
    ample opportunities for adjusting each step of the analysis.
  documentation:
  - note: null
    type:
    - User manual
    url: http://trend.evobionet.com/help
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Protein sequence alignment
        uri: http://edamontology.org/data_1384
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
    - data:
        term: Sequence set (protein)
        uri: http://edamontology.org/data_1233
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
    - data:
        term: Phylogenetic tree
        uri: http://edamontology.org/data_0872
      format:
      - term: newick
        uri: http://edamontology.org/format_1910
    - data:
        term: NCBI locus tag
        uri: http://edamontology.org/data_1900
      format:
      - term: Textual format
        uri: http://edamontology.org/format_2330
    - data:
        term: RefSeq accession (protein)
        uri: http://edamontology.org/data_2385
      format: []
    note: null
    operation:
    - term: Multiple sequence alignment
      uri: http://edamontology.org/operation_0492
    - term: Phylogenetic inference
      uri: http://edamontology.org/operation_0323
    - term: Sequence clustering
      uri: http://edamontology.org/operation_0291
    - term: Sequence classification
      uri: http://edamontology.org/operation_2995
    - term: Protein domain recognition
      uri: http://edamontology.org/operation_0246
    - term: Protein feature detection
      uri: http://edamontology.org/operation_3092
    output:
    - data:
        term: Protein sequence alignment
        uri: http://edamontology.org/data_1384
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
    - data:
        term: Phylogenetic tree
        uri: http://edamontology.org/data_0872
      format:
      - term: newick
        uri: http://edamontology.org/format_1910
    - data:
        term: Protein features
        uri: http://edamontology.org/data_1277
      format:
      - term: JSON
        uri: http://edamontology.org/format_3464
    - data:
        term: Image
        uri: http://edamontology.org/data_2968
      format:
      - term: SVG
        uri: http://edamontology.org/format_3604
    - data:
        term: Sequence cluster (protein)
        uri: http://edamontology.org/data_1245
      format:
      - term: JSON
        uri: http://edamontology.org/format_3464
  homepage: http://trend.evobionet.com/
  homepage_status: 0
  language: []
  lastUpdate: '2024-12-17T20:42:49.942166Z'
  license: null
  link: []
  maturity: null
  name: TREND Protein Evolution Function
  operatingSystem: []
  otherID: []
  owner: vadim
  publication:
  - doi: 10.1093/nar/gkaa243
    metadata:
      abstract: Key steps in a computational study of protein function involve analysis
        of (i) relationships between homologous proteins, (ii) protein domain architecture
        and (iii) gene neighborhoods the corresponding proteins are encoded in. Each
        of these steps requires a separate computational task and sets of tools. Currently
        in order to relate protein features and gene neighborhoods information to
        phylogeny, researchers need to prepare all the necessary data and combine
        them by hand, which is time-consuming and error-prone. Here, we present a
        new platform, TREND (tree-based exploration of neighborhoods and domains),
        which can perform all the necessary steps in automated fashion and put the
        derived information into phylogenomic context, thus making evolutionary based
        protein function analysis more efficient. A rich set of adjustable components
        allows a user to run the computational steps specific to his task. TREND is
        freely available at http://trend.zhulinlab.org.
      authors:
      - name: Gumerov V.M.
      - name: Zhulin I.B.
      citationCount: 33
      date: '2021-01-01T00:00:00Z'
      journal: Nucleic Acids Research
      title: 'TREND: a platform for exploring protein function in prokaryotes based
        on phylogenetic, domain architecture and gene neighborhood analyses'
    note: null
    pmcid: PMC7319448
    pmid: '32282909'
    type:
    - Primary
    version: null
  - doi: 10.1093/nar/gkac034
    metadata:
      abstract: TheURL address of the web server published in this article has been
        changed fromhttp://trend.zhulinlab.org to http://trend. evobionet.com/.
      authors:
      - name: Gumerov V.M.
      - name: Zhulin I.B.
      citationCount: 6
      date: '2022-02-22T00:00:00Z'
      journal: Nucleic Acids Research
      title: 'Erratum: TREND: A platform for exploring protein function in prokaryotes
        based on phylogenetic, domain architecture and gene neighborhood analyses
        (Nucleic Acids Research DOI: 10.1093/nar/gkaa243)'
    note: 'Can be also accessed at this URL: https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkac034/6517937'
    pmcid: PMC8860576
    pmid: '35100406'
    type:
    - Other
    version: null
  relation: []
  toolType:
  - Web service
  topic:
  - term: Evolutionary biology
    uri: http://edamontology.org/topic_3299
  - term: Phylogeny
    uri: http://edamontology.org/topic_0084
  - term: Microbiology
    uri: http://edamontology.org/topic_3301
  - term: Protein sites, features and motifs
    uri: http://edamontology.org/topic_3510
  - term: Functional genomics
    uri: http://edamontology.org/topic_0085
  - term: Phylogenomics
    uri: http://edamontology.org/topic_0194
  - term: Bioinformatics
    uri: http://edamontology.org/topic_0091
  validated: 0
  version: []
- accessibility: null
  additionDate: '2015-08-24T10:00:36Z'
  biotoolsCURIE: biotools:cofactory
  biotoolsID: cofactory
  collectionID: []
  confidence_flag: null
  cost: Free of charge (with restrictions)
  credit:
  - email: null
    fundrefid: null
    gridid: null
    name: CBS
    note: null
    orcidid: null
    rorid: null
    typeEntity: Institute
    typeRole:
    - Provider
    url: null
  - email: tnp@cbs.dtu.dk
    fundrefid: null
    gridid: null
    name: Thomas Nordahl Petersen
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: null
  description: Identification of Rossmann folds and prediction of FAD, NAD and NADP
    specificity.
  documentation:
  - note: null
    type:
    - General
    url: http://www.cbs.dtu.dk/services/Cofactory/instructions.php
  download:
  - note: null
    type: Source code
    url: http://www.cbs.dtu.dk/services/doc/cofactory-1.0.readme
    version: null
  - note: null
    type: Binaries
    url: http://www.cbs.dtu.dk/services/doc/cofactory-1.0.readme
    version: null
  editPermission:
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    type: private
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  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Sequence
        uri: http://edamontology.org/data_2044
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
    note: identifies Rossmann fold sequence domains and predicts their specificity
      for the cofactors FAD, NAD or NADP
    operation:
    - term: Prediction and recognition
      uri: http://edamontology.org/operation_2423
    output:
    - data:
        term: Protein features
        uri: http://edamontology.org/data_1277
      format:
      - term: Textual format
        uri: http://edamontology.org/format_2330
  homepage: http://cbs.dtu.dk/services/Cofactory/
  homepage_status: 0
  language: []
  lastUpdate: '2024-11-25T16:22:09.216410Z'
  license: Other
  link:
  - note: null
    type:
    - Repository
    url: http://www.cbs.dtu.dk/services/doc/cofactory-1.0.readme
  - note: null
    type:
    - Software catalogue
    url: http://cbs.dtu.dk/services
  maturity: Emerging
  name: Cofactory
  operatingSystem:
  - Linux
  otherID: []
  owner: CBS
  publication:
  - doi: 10.1002/prot.24536
    metadata: null
    note: null
    pmcid: null
    pmid: '24523134'
    type:
    - Primary
    version: null
  relation: []
  toolType:
  - Web application
  topic:
  - term: Protein sites, features and motifs
    uri: http://edamontology.org/topic_3510
  validated: 1
  version:
  - '2.1'
- accessibility: null
  additionDate: '2016-06-02T02:47:10Z'
  biotoolsCURIE: biotools:msa
  biotoolsID: msa
  collectionID:
  - Rostlab tools
  - Bioconductor
  - BioJS
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: null
    fundrefid: null
    gridid: null
    name: Sebastian Wilzbach
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Ian Sillitoe
    note: null
    orcidid: null
    rorid: null
    typeEntity: null
    typeRole:
    - Contributor
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Guy Yachdav
    note: null
    orcidid: null
    rorid: null
    typeEntity: null
    typeRole:
    - Contributor
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Benedikt Rauscher
    note: null
    orcidid: null
    rorid: null
    typeEntity: null
    typeRole:
    - Contributor
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Tatyana Goldberg
    note: null
    orcidid: null
    rorid: null
    typeEntity: null
    typeRole:
    - Contributor
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Technische Universität München
    note: null
    orcidid: null
    rorid: null
    typeEntity: Institute
    typeRole:
    - Provider
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Google Summer of Code (GSoC) 2014
    note: null
    orcidid: null
    rorid: null
    typeEntity: Funding agency
    typeRole:
    - Contributor
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: BioJS
    note: null
    orcidid: null
    rorid: null
    typeEntity: Institute
    typeRole:
    - Provider
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: null
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: http://github.com/wilzbach/msa
  - email: bodenhofer@bioinf.jku.at
    fundrefid: null
    gridid: null
    name: Ulrich Bodenhofer
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: null
  description: Display multiple-sequence alignment. The tool is also available as
    R/BioConductor interface to the multiple sequence alignment algorithms ClustalW,
    ClustalOmega, and Muscle. All three algorithms are integrated in the package,
    therefore, they do not depend on any external software tools and are available
    for all major platforms.
  documentation:
  - note: null
    type:
    - Terms of use
    url: https://github.com/wilzbach/msa/blob/master/LICENSE
  - note: null
    type:
    - General
    url: http://msa.biojs.net
  download:
  - note: null
    type: Source code
    url: https://github.com/wilzbach/msa
    version: null
  - note: null
    type: Binaries
    url: https://cdn.bio.sh/
    version: null
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Sequence alignment
        uri: http://edamontology.org/data_0863
      format:
      - term: ClustalW format
        uri: http://edamontology.org/format_1982
      - term: FASTA-aln
        uri: http://edamontology.org/format_1984
    note: 'Visualizes multiple sequence alignment, calculates conservation, shows
      sequence logo, applies multiple color schemes A multiple sequence alignment
      (ClustalW, FASTA, ...) Exports selected sequences and regions from the alignment
      Images are exported in PNG Export sequences in FASTA format Export features
      in GFF

      NOTE: Actually, all these output types of data should instead be under separate
      "constant" operations, while the visualisation should be an unary operation,
      perhaps without an output.'
    operation:
    - term: Sequence visualisation
      uri: http://edamontology.org/operation_0564
    output:
    - data:
        term: Sequence alignment
        uri: http://edamontology.org/data_0863
      format:
      - term: FASTA-aln
        uri: http://edamontology.org/format_1984
    - data:
        term: Sequence alignment image
        uri: http://edamontology.org/data_1711
      format:
      - term: Image format
        uri: http://edamontology.org/format_3547
    - data:
        term: Sequence set
        uri: http://edamontology.org/data_0850
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
    - data:
        term: Feature table
        uri: http://edamontology.org/data_1270
      format:
      - term: GFF
        uri: http://edamontology.org/format_2305
  - cmd: null
    input:
    - data:
        term: Nucleic acid sequence
        uri: http://edamontology.org/data_2977
      format:
      - term: nbrf/pir
        uri: http://edamontology.org/format_1948
      - term: FASTA
        uri: http://edamontology.org/format_1929
      - term: GCG
        uri: http://edamontology.org/format_1935
      - term: PHYLIP format
        uri: http://edamontology.org/format_1997
      - term: EMBL format
        uri: http://edamontology.org/format_1927
      - term: GenBank format
        uri: http://edamontology.org/format_1936
    - data:
        term: Protein sequence
        uri: http://edamontology.org/data_2976
      format:
      - term: nbrf/pir
        uri: http://edamontology.org/format_1948
      - term: FASTA
        uri: http://edamontology.org/format_1929
      - term: GCG
        uri: http://edamontology.org/format_1935
      - term: PHYLIP format
        uri: http://edamontology.org/format_1997
      - term: EMBL format
        uri: http://edamontology.org/format_1927
      - term: GenBank format
        uri: http://edamontology.org/format_1936
    note: null
    operation:
    - term: Multiple sequence alignment
      uri: http://edamontology.org/operation_0492
    output:
    - data:
        term: Sequence alignment report
        uri: http://edamontology.org/data_0867
      format:
      - term: ClustalW format
        uri: http://edamontology.org/format_1982
      - term: FASTA
        uri: http://edamontology.org/format_1929
      - term: PHYLIP format
        uri: http://edamontology.org/format_1997
      - term: PDF
        uri: http://edamontology.org/format_3508
  homepage: http://msa.biojs.net
  homepage_status: 0
  language:
  - JavaScript
  lastUpdate: '2024-11-25T16:17:03.898741Z'
  license: Apache-2.0
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/wilzbach/msa
  - note: null
    type:
    - Software catalogue
    url: http://biojs.io/
  - note: null
    type:
    - Helpdesk
    url: http://github.com/wilzbach/msa
  - note: null
    type:
    - Mirror
    url: http://www.bioinf.jku.at/software/msa/
  maturity: Mature
  name: msa
  operatingSystem:
  - Linux
  - Windows
  - Mac
  otherID: []
  owner: BioJS
  publication:
  - doi: 10.1093/bioinformatics/btw474
    metadata: null
    note: null
    pmcid: PMC5181560
    pmid: '27412096'
    type:
    - Primary
    version: null
  - doi: 10.1093/bioinformatics/btv494
    metadata: null
    note: null
    pmcid: null
    pmid: '26315911'
    type:
    - Other
    version: null
  relation: []
  toolType:
  - Command-line tool
  - Library
  topic:
  - term: Sequence analysis
    uri: http://edamontology.org/topic_0080
  - term: Sequence sites, features and motifs
    uri: http://edamontology.org/topic_0160
  - term: Phylogenetics
    uri: http://edamontology.org/topic_3293
  - term: Sequencing
    uri: http://edamontology.org/topic_3168
  validated: 1
  version:
  - 1.0.0
- accessibility: null
  additionDate: '2015-01-21T15:12:23Z'
  biotoolsCURIE: biotools:crispi
  biotoolsID: crispi
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: null
    fundrefid: null
    gridid: null
    name: GenOuest
    note: null
    orcidid: null
    rorid: null
    typeEntity: Institute
    typeRole:
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    url: null
  - email: support@genouest.org
    fundrefid: null
    gridid: null
    name: GenOuest platform
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: http://www.genouest.org
  description: A CRISPR Interactive database.
  documentation:
  - note: null
    type:
    - General
    url: http://genoweb1.irisa.fr/Serveur-GPO/outils/repeatsAnalysis/CRISPR/help/crispri.pdf
  download: []
  editPermission:
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  elixirNode: []
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  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Sequence
        uri: http://edamontology.org/data_2044
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
    note: A CRISPR Interactive database
    operation:
    - term: Sequence database search
      uri: http://edamontology.org/operation_0338
    output:
    - data:
        term: Sequence alignment
        uri: http://edamontology.org/data_0863
      format:
      - term: Textual format
        uri: http://edamontology.org/format_2330
  homepage: http://crispi.genouest.org/
  homepage_status: 0
  language: []
  lastUpdate: '2024-11-25T16:06:25.068541Z'
  license: null
  link: []
  maturity: Mature
  name: Crispi
  operatingSystem:
  - Linux
  - Windows
  - Mac
  otherID: []
  owner: GenOuest
  publication:
  - doi: 10.1093/bioinformatics/btp586
    metadata: null
    note: null
    pmcid: PMC2788928
    pmid: '19846435'
    type:
    - Primary
    version: null
  relation: []
  toolType:
  - Database portal
  topic:
  - term: Sequence sites, features and motifs
    uri: http://edamontology.org/topic_0160
  validated: 1
  version: []
- accessibility: null
  additionDate: '2015-01-21T15:12:23Z'
  biotoolsCURIE: biotools:plast
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  collectionID: []
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  cost: Free of charge
  credit:
  - email: null
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    gridid: null
    name: GenOuest
    note: null
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  - email: lavenier@irisa.fr
    fundrefid: null
    gridid: null
    name: Dominique Lavenier
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: null
  description: Parallel Local Alignment Search Tool for Database Comparison.
  documentation:
  - note: null
    type:
    - General
    url: https://plast.inria.fr/
  download: []
  editPermission:
    authors: []
    type: private
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  elixirNode: []
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  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Sequence
        uri: http://edamontology.org/data_2044
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
    - data:
        term: Sequence
        uri: http://edamontology.org/data_2044
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
    note: Sequence alignment
    operation:
    - term: Local alignment
      uri: http://edamontology.org/operation_0495
    output:
    - data:
        term: Sequence alignment
        uri: http://edamontology.org/data_0863
      format:
      - term: Textual format
        uri: http://edamontology.org/format_2330
  homepage: http://www.irisa.fr/symbiose/projects/plast/
  homepage_status: 0
  language: []
  lastUpdate: '2024-11-25T16:06:23.702130Z'
  license: CECILL-2.0
  link: []
  maturity: Mature
  name: Plast
  operatingSystem:
  - Linux
  - Windows
  - Mac
  otherID: []
  owner: GenOuest
  publication:
  - doi: 10.1186/1471-2105-10-329
    metadata: null
    note: null
    pmcid: PMC2770072
    pmid: '19821978'
    type:
    - Primary
    version: null
  relation: []
  toolType:
  - Command-line tool
  topic:
  - term: Sequence analysis
    uri: http://edamontology.org/topic_0080
  validated: 1
  version:
  - '1.0'
- accessibility: null
  additionDate: '2015-01-21T15:12:22Z'
  biotoolsCURIE: biotools:mapsembler
  biotoolsID: mapsembler
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: null
    fundrefid: null
    gridid: null
    name: GenOuest
    note: null
    orcidid: null
    rorid: null
    typeEntity: Institute
    typeRole:
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  - 1.0.8
- accessibility: null
  additionDate: '2017-07-26T20:17:02Z'
  biotoolsCURIE: biotools:pred-tat
  biotoolsID: pred-tat
  collectionID: []
  confidence_flag: null
  cost: null
  credit:
  - email: pbagos@compgen.org
    fundrefid: null
    gridid: null
    name: Pantelis Bagos
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: http://www.compgen.org/people/pbagos
  description: PRED-TAT is a tool that takes a protein sequence as input and discriminating
    Sec from Tat signal peptides and predicting their cleavage sites.
  documentation:
  - note: null
    type:
    - General
    url: http://www.compgen.org/tools/PRED-TAT
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Sequence
        uri: http://edamontology.org/data_2044
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
    note: null
    operation:
    - term: Protein signal peptide detection
      uri: http://edamontology.org/operation_0418
    - term: Transmembrane protein analysis
      uri: http://edamontology.org/operation_0270
    - term: Transmembrane protein prediction
      uri: http://edamontology.org/operation_0269
    - term: Protein cleavage site prediction
      uri: http://edamontology.org/operation_0422
    output:
    - data:
        term: Sequence report
        uri: http://edamontology.org/data_2955
      format:
      - term: Textual format
        uri: http://edamontology.org/format_2330
  homepage: http://www.compgen.org/tools/PRED-TAT
  homepage_status: 0
  language: []
  lastUpdate: '2024-11-25T15:44:18.398512Z'
  license: null
  link: []
  maturity: null
  name: PRED-TAT
  operatingSystem:
  - Linux
  - Windows
  - Mac
  otherID: []
  owner: itamposis
  publication:
  - doi: 10.1093/bioinformatics/btq530
    metadata: null
    note: null
    pmcid: null
    pmid: '20847219'
    type: []
    version: null
  relation: []
  toolType:
  - Web application
  topic:
  - term: Sequence sites, features and motifs
    uri: http://edamontology.org/topic_0160
  validated: 1
  version:
  - '1.1'
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