count: 224
list:
- accessibility: Open access (with restrictions)
  additionDate: '2021-03-31T15:26:55Z'
  biotoolsCURIE: biotools:biomas_bioinformatic_analysis_of_metagenomic_amplicons
  biotoolsID: biomas_bioinformatic_analysis_of_metagenomic_amplicons
  collectionID: []
  confidence_flag: tool
  cost: Free of charge (with restrictions)
  credit:
  - email: b.fosso@ibiom.cnr.it
    fundrefid: null
    gridid: null
    name: Bruno Fosso
    note: Researcher at CNR-IBIOM
    orcidid: https://orcid.org/0000-0003-2324-086X
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    url: null
  - email: graziano.pesole@uniba.it
    fundrefid: null
    gridid: null
    name: Graziano Pesole
    note: Full Professor of Molecular Biology at University of Bari
    orcidid: https://orcid.org/0000-0003-3663-0859
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: null
  - email: m.santamaria@ibiom.cnr.it
    fundrefid: null
    gridid: null
    name: Monica Santamaria
    note: Researcher at CNR-IBIOM
    orcidid: https://orcid.org/0000-0003-1488-6052
    rorid: null
    typeEntity: Person
    typeRole:
    - Contributor
    url: null
  description: BioMaS is a friendly pipeline for Meta-barcoding HTS data analysis
    specifically designed for users without particular computing skills.
  documentation: []
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity:
  - Marine Metagenomics
  elixirNode:
  - Italy
  elixirPlatform:
  - Tools
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Nucleic acid sequence alignment
        uri: http://edamontology.org/data_1383
      format:
      - 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: newick
        uri: http://edamontology.org/format_1910
  - cmd: null
    input:
    - data:
        term: DNA sequence
        uri: http://edamontology.org/data_3494
      format:
      - term: FASTQ
        uri: http://edamontology.org/format_1930
    note: null
    operation:
    - term: Sequence merging
      uri: http://edamontology.org/operation_0232
    output:
    - data:
        term: DNA sequence
        uri: http://edamontology.org/data_3494
      format:
      - term: FASTQ
        uri: http://edamontology.org/format_1930
  - cmd: null
    input:
    - data:
        term: DNA sequence
        uri: http://edamontology.org/data_3494
      format:
      - term: FASTQ
        uri: http://edamontology.org/format_1930
    note: null
    operation:
    - term: Global alignment
      uri: http://edamontology.org/operation_0496
    output:
    - data:
        term: Nucleic acid sequence alignment
        uri: http://edamontology.org/data_1383
      format:
      - term: SAM
        uri: http://edamontology.org/format_2573
  homepage: http://itsonewb.cloud.ba.infn.it/galaxy/tool_runner?tool_id=biomas2_wrapper
  homepage_status: 0
  language:
  - Bash
  - Python
  lastUpdate: '2026-01-27T17:22:28.785300Z'
  license: Not licensed
  link: []
  maturity: Emerging
  name: BioMaS (Bioinformatic analysis of Metagenomic amplicons)
  operatingSystem:
  - Linux
  - Mac
  - Windows
  otherID: []
  owner: bfosso
  publication:
  - doi: 10.1186/s12859-015-0595-z
    metadata: null
    note: null
    pmcid: PMC4486701
    pmid: '26130132'
    type:
    - Method
    version: null
  relation: []
  toolType:
  - Web application
  topic:
  - term: Omics
    uri: http://edamontology.org/topic_3391
  validated: 0
  version:
  - '1.0'
- accessibility: null
  additionDate: '2016-11-28T10:07:17Z'
  biotoolsCURIE: biotools:siena
  biotoolsID: siena
  collectionID:
  - de.NBI
  - COVID-19
  confidence_flag: null
  cost: null
  credit:
  - email: null
    fundrefid: null
    gridid: null
    name: University of Hamburg - Center for Bioinformatics
    note: null
    orcidid: null
    rorid: null
    typeEntity: Institute
    typeRole:
    - Provider
    url: null
  - email: rarey-office@zbh.uni-hamburg.de
    fundrefid: null
    gridid: null
    name: null
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: null
  description: Search for homologous protein binding sites structures in the Protein
    Data Bank. The tool allows an automated assembly and preprocessing of protein
    structure ensembles supporting protein flexibility and point mutation analyses
    as well as structure-based virtual screening.
  documentation:
  - note: null
    type:
    - General
    url: http://proteinsplus.zbh.uni-hamburg.de/help/index
  download: []
  editPermission:
    authors:
    - Bietz
    - ehrt
    type: group
  elixirCommunity:
  - 3D-BioInfo
  elixirNode:
  - Germany
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Protein structure
        uri: http://edamontology.org/data_1460
      format:
      - term: PDB
        uri: http://edamontology.org/format_1476
    note: statistics
    operation:
    - term: Clustering
      uri: http://edamontology.org/operation_3432
    - term: Structure database search
      uri: http://edamontology.org/operation_0339
    - term: Sequence assembly
      uri: http://edamontology.org/operation_0310
    - term: Structure alignment
      uri: http://edamontology.org/operation_0295
    - term: Protein flexibility and motion analysis
      uri: http://edamontology.org/operation_0244
    output:
    - data:
        term: Protein structure
        uri: http://edamontology.org/data_1460
      format:
      - term: PDB
        uri: http://edamontology.org/format_1476
    - data:
        term: Sequence alignment (protein)
        uri: http://edamontology.org/data_1384
      format: []
    - data:
        term: Root-mean-square deviation
        uri: http://edamontology.org/data_1497
      format: []
  homepage: http://proteinsplus.zbh.uni-hamburg.de/#siena
  homepage_status: 0
  language: []
  lastUpdate: '2025-12-23T14:50:32.227556Z'
  license: null
  link: []
  maturity: null
  name: SIENA
  operatingSystem:
  - Linux
  - Windows
  - Mac
  otherID: []
  owner: ehrt
  publication:
  - doi: 10.1021/acs.jcim.5b00588
    metadata:
      abstract: Structural flexibility of proteins has an important influence on molecular
        recognition and enzymatic function. In modeling, structure ensembles are therefore
        often applied as a valuable source of alternative protein conformations. However,
        their usage is often complicated by structural artifacts and inconsistent
        data annotation. Here, we present SIENA, a new computational approach for
        the automated assembly and preprocessing of protein binding site ensembles.
        Starting with an arbitrarily defined binding site in a single protein structure,
        SIENA searches for alternative conformations of the same or sequentially closely
        related binding sites. The method is based on an indexed database for identifying
        perfect k-mer matches and a recently published algorithm for the alignment
        of protein binding site conformations. Furthermore, SIENA provides a new algorithm
        for the interaction-based selection of binding site conformations which aims
        at covering all known ligand-binding geometries. Various experiments highlight
        that SIENA is able to generate comprehensive and well selected binding site
        ensembles improving the compatibility to both known and unconsidered ligand
        molecules. Starting with the whole PDB as data source, the computation time
        of the whole ensemble generation takes only a few seconds. SIENA is available
        via a Web service at www.zbh.uni-hamburg.de/siena.
      authors:
      - name: Bietz S.
      - name: Rarey M.
      citationCount: 37
      date: '2016-01-25T00:00:00Z'
      journal: Journal of Chemical Information and Modeling
      title: 'SIENA: Efficient Compilation of Selective Protein Binding Site Ensembles'
    note: null
    pmcid: null
    pmid: '26759067'
    type:
    - Method
    version: null
  - doi: 10.1021/acs.jcim.5b00210
    metadata:
      abstract: The usage of conformational ensembles constitutes a widespread technique
        for the consideration of protein flexibility in computational biology. When
        experimental structures are applied for this purpose, alignment techniques
        are usually required in dealing with structural deviations and annotation
        inconsistencies. Moreover, many application scenarios focus on protein ligand
        binding sites. Here, we introduce our new alignment algorithm ASCONA that
        has been specially geared to the problem of aligning multiple conformations
        of sequentially similar binding sites. Intense efforts have been directed
        to an accurate detection of highly flexible backbone deviations, multiple
        binding site matches within a single structure, and a reliable, but at the
        same time highly efficient, search algorithm. In contrast, most available
        alignment methods rather target other issues, e.g., the global alignment of
        distantly related proteins that share structurally conserved regions. For
        conformational ensembles, this might not only result in an overhead of computation
        time but could also affect the achieved accuracy, especially for more complicated
        cases as highly flexible proteins. ASCONA was evaluated on a test set containing
        1107 structures of 65 diverse proteins. In all cases, ASCONA was able to correctly
        align the binding site at an average alignment computation time of 4 ms per
        target. Furthermore, no false positive matches were observed when searching
        the same query sites in the structures of other proteins. ASCONA proved to
        cope with highly deviating backbone structures and to tolerate structural
        gaps and moderate mutation rates. ASCONA is available free of charge for academic
        use at http://www.zbh.uni-hamburg.de/ascona. (Figure Presented).
      authors:
      - name: Bietz S.
      - name: Rarey M.
      citationCount: 15
      date: '2015-08-24T00:00:00Z'
      journal: Journal of Chemical Information and Modeling
      title: 'ASCONA: Rapid Detection and Alignment of Protein Binding Site Conformations'
    note: null
    pmcid: null
    pmid: '26098831'
    type:
    - Method
    version: null
  relation: []
  toolType:
  - Web application
  topic:
  - term: Protein binding sites
    uri: http://edamontology.org/topic_3534
  - term: Structure analysis
    uri: http://edamontology.org/topic_0081
  - term: Drug discovery
    uri: http://edamontology.org/topic_3336
  validated: 1
  version: []
- accessibility: Open access
  additionDate: '2018-07-29T10:31:55Z'
  biotoolsCURIE: biotools:d-genies
  biotoolsID: d-genies
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: null
    fundrefid: null
    gridid: null
    name: Floréal Cabanettes
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    url: null
  - email: christophe.klopp@inrae.fr
    fundrefid: null
    gridid: null
    name: Christophe Klopp
    note: null
    orcidid: https://orcid.org/0000-0001-7126-5477
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Philippe Bordron
    note: null
    orcidid: https://orcid.org/0000-0003-1975-0920
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    - Developer
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Vincent Dominguez
    note: null
    orcidid: null
    rorid: null
    typeEntity: null
    typeRole:
    - Developer
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: GenoToul bioinformatics facility
    note: null
    orcidid: null
    rorid: null
    typeEntity: Division
    typeRole:
    - Provider
    url: http://bioinfo.genotoul.fr/
  description: D-GENIES – for Dot plot large Genomes in an Interactive, Efficient
    and Simple way – is an online tool designed to compare two genomes. It supports
    large genome and you can interact with the dot plot to improve the visualization.
  documentation:
  - note: null
    type:
    - General
    url: https://dgenies.readthedocs.io/en/latest/index.html
  download: []
  editPermission:
    authors:
    - pbordron
    type: group
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: DNA sequence
        uri: http://edamontology.org/data_3494
      format: []
    - data:
        term: DNA sequence
        uri: http://edamontology.org/data_3494
      format: []
    note: null
    operation:
    - term: Genome alignment
      uri: http://edamontology.org/operation_3182
    output:
    - data:
        term: Nucleic acid sequence alignment
        uri: http://edamontology.org/data_1383
      format: []
    - data:
        term: Sequence similarity plot
        uri: http://edamontology.org/data_2161
      format: []
  - cmd: null
    input:
    - data:
        term: Nucleic acid sequence alignment
        uri: http://edamontology.org/data_1383
      format: []
    note: null
    operation:
    - term: Dot plot plotting
      uri: http://edamontology.org/operation_0490
    output:
    - data:
        term: Sequence similarity plot
        uri: http://edamontology.org/data_2161
      format: []
  homepage: https://dgenies.toulouse.inrae.fr/
  homepage_status: 0
  language:
  - Python
  - Shell
  lastUpdate: '2025-12-18T10:02:18.098079Z'
  license: GPL-3.0
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/genotoul-bioinfo/dgenies
  maturity: Mature
  name: D-GENIES
  operatingSystem:
  - Mac
  - Linux
  otherID: []
  owner: d.gabrielaitis
  publication:
  - doi: 10.7717/peerj.4958
    metadata:
      abstract: ''
      authors: []
      citationCount: 493
      date: '2018-01-01T00:00:00Z'
      journal: PeerJ
      title: 'D-GENIES: Dot plot large genomes in an interactive, efficient and simple
        way'
    note: null
    pmcid: PMC5991294
    pmid: '29888139'
    type:
    - Primary
    version: null
  relation: []
  toolType:
  - Web application
  - Command-line tool
  topic:
  - term: Genomics
    uri: http://edamontology.org/topic_0622
  - term: Data visualisation
    uri: http://edamontology.org/topic_0092
  - term: Sequence analysis
    uri: http://edamontology.org/topic_0080
  validated: 1
  version: []
- 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:
    authors:
    - ben_s
    - jimprocter
    type: group
  elixirCommunity: []
  elixirNode:
  - UK
  elixirPlatform:
  - Tools
  - Interoperability
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Sequence alignment
        uri: http://edamontology.org/data_0863
      format:
      - term: nbrf/pir
        uri: http://edamontology.org/format_1948
      - term: FASTA
        uri: http://edamontology.org/format_1929
      - term: FASTA-aln
        uri: http://edamontology.org/format_1984
      - term: Pileup
        uri: http://edamontology.org/format_3015
      - term: GFF2-seq
        uri: http://edamontology.org/format_1938
      - term: BLC
        uri: http://edamontology.org/format_3313
      - term: RNAML
        uri: http://edamontology.org/format_3311
      - term: Format
        uri: http://edamontology.org/format_1915
      - term: BioJSON (Jalview)
        uri: http://edamontology.org/format_3774
      - term: ClustalW format
        uri: http://edamontology.org/format_1982
      - term: mmCIF
        uri: http://edamontology.org/format_1477
      - term: PHYLIP format
        uri: http://edamontology.org/format_1997
      - term: VCF
        uri: http://edamontology.org/format_3016
      - term: Stockholm format
        uri: http://edamontology.org/format_1961
      - term: GFF3-seq
        uri: http://edamontology.org/format_1939
      - term: GCG MSF
        uri: http://edamontology.org/format_1947
    - 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 alignment editing
      uri: http://edamontology.org/operation_3081
    - term: Phylogenetic tree analysis
      uri: http://edamontology.org/operation_0324
    - term: Sequence visualisation
      uri: http://edamontology.org/operation_0564
    output:
    - data:
        term: Sequence alignment
        uri: http://edamontology.org/data_0863
      format:
      - term: nbrf/pir
        uri: http://edamontology.org/format_1948
      - term: FASTA
        uri: http://edamontology.org/format_1929
      - term: Pileup
        uri: http://edamontology.org/format_3015
      - term: BLC
        uri: http://edamontology.org/format_3313
      - term: BioJSON (Jalview)
        uri: http://edamontology.org/format_3774
      - term: ClustalW format
        uri: http://edamontology.org/format_1982
      - term: JSON
        uri: http://edamontology.org/format_3464
      - term: PHYLIP format
        uri: http://edamontology.org/format_1997
      - term: Stockholm format
        uri: http://edamontology.org/format_1961
      - term: GCG MSF
        uri: http://edamontology.org/format_1947
    - data:
        term: Plot
        uri: http://edamontology.org/data_2884
      format:
      - term: EPS
        uri: http://edamontology.org/format_3466
      - term: Format
        uri: http://edamontology.org/format_1915
      - term: HTML
        uri: http://edamontology.org/format_2331
      - term: SVG
        uri: http://edamontology.org/format_3604
      - term: PNG
        uri: http://edamontology.org/format_3603
  homepage: https://www.jalview.org/
  homepage_status: 0
  language: []
  lastUpdate: '2025-12-11T14:16:30.074724Z'
  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://gitlab.jalview.org/jalview/jalview.git
  - 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
  - note: null
    type:
    - Social media
    url: https://www.linkedin.com/company/104771886/
  maturity: Mature
  name: Jalview
  operatingSystem:
  - Mac
  - Linux
  - Windows
  otherID: []
  owner: ben_s
  publication:
  - doi: 10.1093/bioinformatics/btp033
    metadata:
      abstract: ''
      authors: []
      citationCount: 7717
      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:
  - biotoolsID: jabaws
    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
  - biotoolsID: 3d-beacons
    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:
  - 2.11.5.1
- accessibility: Open access
  additionDate: '2016-09-30T15:59:05Z'
  biotoolsCURIE: biotools:silva
  biotoolsID: silva
  collectionID:
  - de.NBI
  - de.NBI-biodata
  - DSMZ Digital Diversity
  confidence_flag: tool
  cost: Free of charge
  credit:
  - 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:
    - Provider
    url: https://www.dsmz.de
  - email: contact@arb-silva.de
    fundrefid: null
    gridid: grid.507782.f
    name: SILVA Team
    note: null
    orcidid: null
    rorid: 027z9pz32
    typeEntity: Division
    typeRole:
    - Primary contact
    url: https://www.arb-silva.de/contact/team/
  description: SILVA provides comprehensive, quality checked and regularly updated
    datasets of aligned small (16S/18S, SSU) and large subunit (23S/28S, LSU) ribosomal
    RNA (rRNA) sequences for all three domains of life (Bacteria, Archaea and Eukaryota).
  documentation:
  - note: null
    type:
    - Terms of use
    url: https://www.arb-silva.de/silva-license-information/
  - note: null
    type:
    - Citation instructions
    url: https://www.arb-silva.de/contact/
  - note: null
    type:
    - General
    url: https://www.arb-silva.de/documentation/
  - note: null
    type:
    - FAQ
    url: https://www.arb-silva.de/documentation/faqs/
  download:
  - note: SILVA dataset archive
    type: Downloads page
    url: https://www.arb-silva.de/download/archive/
    version: null
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    input:
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        uri: http://edamontology.org/data_1097
      format:
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        uri: http://edamontology.org/format_1964
    - data:
        term: Taxon
        uri: http://edamontology.org/data_1868
      format:
      - term: plain text format (unformatted)
        uri: http://edamontology.org/format_1964
    - data:
        term: Strain name
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      format:
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        uri: http://edamontology.org/format_1964
    - data:
        term: Article ID
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        term: Organism name
        uri: http://edamontology.org/data_2909
      format:
      - term: plain text format (unformatted)
        uri: http://edamontology.org/format_1964
    note: The search and retrieval functions of the SILVA website can be used to build
      custom subsets of sequences. In addition to simple searches e.g. for accession
      numbers, organism names, taxonomic entities, or publication DOI/PubMed IDs,
      complex queries over several database fields using constraints such as sequence
      length or quality values are possible. The results can be sorted according to
      accession numbers, organism names, sequence length, sequence and alignment quality
      and Pintail values. The search results show accession number, organism name,
      sequence length, sequence quality values, taxonomic classifications, and links
      to view the full sequence record on SILVA and on ENA. Sequences found via search
      and added to download cart can be downloaded as FASTA and ARB files.
    operation:
    - term: Query and retrieval
      uri: http://edamontology.org/operation_0224
    output:
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        term: Sequence report
        uri: http://edamontology.org/data_2955
      format:
      - term: HTML
        uri: http://edamontology.org/format_2331
    - data:
        term: Sequence alignment (nucleic acid)
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      format:
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        uri: http://edamontology.org/format_3830
      - term: FASTA-aln
        uri: http://edamontology.org/format_1984
    - data:
        term: Nucleic acid sequence
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      format:
      - term: ARB
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      - term: FASTA-aln
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  - cmd: null
    input:
    - data:
        term: Nucleic acid sequence
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      format:
      - term: nucleotide
        uri: http://edamontology.org/format_1207
    - data:
        term: PCR primers
        uri: http://edamontology.org/data_1240
      format:
      - term: nucleotide
        uri: http://edamontology.org/format_1207
    note: "The SILVA Probe Match and Evaluation Tool detects and displays all occurrences\
      \ of a given probe or primer sequence in the SILVA datasets. \n\nTestPrime allows\
      \ you to evaluate the performance of primer pairs by running an in silico PCR\
      \ on the SILVA databases. From the results of the PCR, TestPrime computes coverages\
      \ for each taxonomic group in all of the taxonomies offered by SILVA."
    operation:
    - term: Primer and probe design
      uri: http://edamontology.org/operation_2419
    output:
    - data:
        term: Report
        uri: http://edamontology.org/data_2048
      format:
      - term: CSV
        uri: http://edamontology.org/format_3752
      - term: HTML
        uri: http://edamontology.org/format_2331
    - data:
        term: Sequence set
        uri: http://edamontology.org/data_0850
      format:
      - term: Binary format
        uri: http://edamontology.org/format_2333
    - data:
        term: Nucleic acid sequence alignment
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    note: The Alignment, Classification and Tree Service (ACT) of SILVA allows to
      align and optionally classify sequences using the SILVA Incremental Aligner
      (SINA). From aligned sequences, (optionally) phylogenetic trees can be inferred
      using FastTree or RAxML.
    operation:
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    - term: Global alignment
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    - term: Taxonomic classification
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    - term: Phylogenetic inference (maximum likelihood and Bayesian methods)
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        term: Taxonomic classification
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      format:
      - term: CSV
        uri: http://edamontology.org/format_3752
  homepage: https://www.arb-silva.de
  homepage_status: 0
  language: []
  lastUpdate: '2025-06-30T13:26:42.882897Z'
  license: CC-BY-4.0
  link:
  - note: SILVA Taxonomy Browser
    type:
    - Service
    url: https://www.arb-silva.de/browser/
  - note: SILVA metadata search
    type:
    - Service
    url: https://www.arb-silva.de/search/
  - note: 'ACT: Alignment, Classification and Tree Service'
    type:
    - Service
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  - note: SILVA Probe Match and Evaluation Tool
    type:
    - Service
    url: https://www.arb-silva.de/search/testprobe/
  - note: SILVA Primer Evaluation Tool
    type:
    - Service
    url: https://www.arb-silva.de/search/testprime/
  - note: Web-based viewer for the SILVA guide trees
    type:
    - Service
    url: https://treeviewer.arb-silva.de/
  maturity: Mature
  name: SILVA rRNA database
  operatingSystem: []
  otherID:
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    value: RRID:SCR_006423
    version: null
  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:
    - Other
    version: null
  - doi: 10.1093/nar/gkm864
    metadata:
      abstract: 'Sequencing ribosomal RNA (rRNA) genes is currently the method of
        choice for phylogenetic reconstruction, nucleic acid based detection and quantification
        of microbial diversity. The ARB software suite with its corresponding rRNA
        datasets has been accepted by researchers worldwide as a standard tool for
        large scale rRNA analysis. However, the rapid increase of publicly available
        rRNA sequence data has recently hampered the maintenance of comprehensive
        and curated rRNA knowledge databases. A new system, SILVA (from Latin silva,
        forest), was implemented to provide a central comprehensive web resource for
        up to date, quality controlled databases of aligned rRNA sequences from the
        Bacteria, Archaea and Eukarya domains. All sequences are checked for anomalies,
        carry a rich set of sequence associated contextual information, have multiple
        taxonomic classifications, and the latest validly described nomenclature.
        Furthermore, two precompiled sequence datasets compatible with ARB are offered
        for download on the SILVA website: (i) the reference (Ref) datasets, comprising
        only high quality, nearly full length sequences suitable for in-depth phylogenetic
        analysis and probe design and (ii) the comprehensive Parc datasets with all
        publicly available rRNA sequences longer than 300 nucleotides suitable for
        biodiversity analyses. The latest publicly available database release 91 (August
        2007) hosts 547 521 sequences split into 461 823 small subunit and 85 689
        large subunit rRNAs. © 2007 The Author(s).'
      authors:
      - name: Pruesse E.
      - name: Quast C.
      - name: Knittel K.
      - name: Fuchs B.M.
      - name: Ludwig W.
      - name: Peplies J.
      - name: Glockner F.O.
      citationCount: 5291
      date: '2007-12-01T00:00:00Z'
      journal: Nucleic Acids Research
      title: 'SILVA: A comprehensive online resource for quality checked and aligned
        ribosomal RNA sequence data compatible with ARB'
    note: null
    pmcid: PMC2175337
    pmid: '17947321'
    type:
    - Other
    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:
    - Other
    version: null
  - doi: 10.1016/j.jbiotec.2017.06.1198
    metadata:
      abstract: SILVA (lat. forest) is a comprehensive web resource, providing services
        around up to date, high-quality datasets of aligned ribosomal RNA gene (rDNA)
        sequences from the Bacteria, Archaea, and Eukaryota domains. SILVA dates back
        to the year 1991 when Dr. Wolfgang Ludwig from the Technical University Munich
        started the integrated software workbench ARB (lat. tree) to support high-quality
        phylogenetic inference and taxonomy based on the SSU and LSU rDNA marker genes.
        At that time, the ARB project maintained both, the sequence reference datasets
        and the software package for data analysis. In 2005, with the massive increase
        of DNA sequence data, the maintenance of the software system ARB and the corresponding
        rRNA databases SILVA was split between Munich and the Microbial Genomics and
        Bioinformatics Research Group in Bremen. ARB has been continuously developed
        to include new features and improve the usability of the workbench. Thousands
        of users worldwide appreciate the seamless integration of common analysis
        tools under a central graphical user interface, in combination with its versatility.
        The first SILVA release was deployed in February 2007 based on the EMBL-EBI/ENA
        release 89. Since then, full SILVA releases offering the database content
        in various flavours are published at least annually, complemented by intermediate
        web-releases where only the SILVA web dataset is updated. SILVA is the only
        rDNA database project worldwide where special emphasis is given to the consistent
        naming of clades of uncultivated (environmental) sequences, where no validly
        described cultivated representatives are available. Also exclusive for SILVA
        is the maintenance of both comprehensive aligned 16S/18S rDNA and 23S/28S
        rDNA sequence datasets. Furthermore, the SILVA alignments and trees were designed
        to include Eukaryota, another unique feature among rDNA databases. With the
        termination of the European Ribosomal RNA Database Project in 2007, the SILVA
        database has become the authoritative rDNA database project for Europe. The
        application spectrum of ARB and SILVA ranges from biodiversity analysis, medical
        diagnostics, to biotechnology and quality control for academia and industry.
      authors:
      - name: Glockner F.O.
      - name: Yilmaz P.
      - name: Quast C.
      - name: Gerken J.
      - name: Beccati A.
      - name: Ciuprina A.
      - name: Bruns G.
      - name: Yarza P.
      - name: Peplies J.
      - name: Westram R.
      - name: Ludwig W.
      citationCount: 635
      date: '2017-11-10T00:00:00Z'
      journal: Journal of Biotechnology
      title: 25 years of serving the community with ribosomal RNA gene reference databases
        and tools
    note: null
    pmcid: null
    pmid: '28648396'
    type:
    - Review
    version: null
  - doi: 10.1186/s12859-017-1841-3
    metadata:
      abstract: 'Background: Phylogenetic trees are an important tool to study the
        evolutionary relationships among organisms. The huge amount of available taxa
        poses difficulties in their interactive visualization. This hampers the interaction
        with the users to provide feedback for the further improvement of the taxonomic
        framework. Results: The SILVA Tree Viewer is a web application designed for
        visualizing large phylogenetic trees without requiring the download of any
        software tool or data files. The SILVA Tree Viewer is based on Web Geographic
        Information Systems (Web-GIS) technology with a PostgreSQL backend. It enables
        zoom and pan functionalities similar to Google Maps. The SILVA Tree Viewer
        enables access to two phylogenetic (guide) trees provided by the SILVA database:
        the SSU Ref NR99 inferred from high-quality, full-length small subunit sequences,
        clustered at 99% sequence identity and the LSU Ref inferred from high-quality,
        full-length large subunit sequences. Conclusions: The Tree Viewer provides
        tree navigation, search and browse tools as well as an interactive feedback
        system to collect any kinds of requests ranging from taxonomy to data curation
        and improving the tool itself.'
      authors:
      - name: Beccati A.
      - name: Gerken J.
      - name: Quast C.
      - name: Yilmaz P.
      - name: Glockner F.O.
      citationCount: 29
      date: '2017-09-30T00:00:00Z'
      journal: BMC Bioinformatics
      title: 'SILVA tree viewer: Interactive web browsing of the SILVA phylogenetic
        guide trees'
    note: null
    pmcid: null
    pmid: null
    type:
    - Other
    version: null
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    type: usedBy
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  topic:
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    uri: http://edamontology.org/topic_0659
  - term: Sequence analysis
    uri: http://edamontology.org/topic_0080
  - term: Phylogenetics
    uri: http://edamontology.org/topic_3293
  - term: Taxonomy
    uri: http://edamontology.org/topic_0637
  - term: Biodiversity
    uri: http://edamontology.org/topic_3050
  - term: Microbiology
    uri: http://edamontology.org/topic_3301
  - term: Probes and primers
    uri: http://edamontology.org/topic_0632
  validated: 1
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- accessibility: Open access
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  description: The Zoonomia Project provides access to genomic data including assemblies,
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        uri: http://edamontology.org/data_1045
      format: []
    note: null
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      format: []
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  owner: adriaan
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  validated: 0
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- accessibility: Open access
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    fundrefid: null
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    note: null
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    rorid: null
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    url: null
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    fundrefid: null
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    name: Josep Lluís Gelpí
    note: null
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    rorid: null
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    typeRole:
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    url: null
  - email: vre@multiscalegenomics.eu
    fundrefid: null
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    url: https://www.multiscalegenomics.eu/
  description: The MuG Virtual Research Environment is an analysis platform for 3D/4D
    genomics analyses. It integrates genomics tools for chromatin dynamics data.
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  - note: null
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        uri: http://edamontology.org/format_1930
      - term: FASTA
        uri: http://edamontology.org/format_1929
    - data:
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      format: []
    note: null
    operation:
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      uri: http://edamontology.org/operation_0292
    - term: Read mapping
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      format:
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  - cmd: null
    input:
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    - data:
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      format:
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    note: null
    operation:
    - term: Nucleic acid structure prediction
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    - term: Modelling and simulation
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      uri: http://edamontology.org/operation_0279
    output:
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      format: []
    - data:
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      format:
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  - cmd: null
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      format:
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    note: null
    operation:
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    - term: DNA-binding protein prediction
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        term: Protein complex
        uri: http://edamontology.org/data_2877
      format:
      - term: PDB
        uri: http://edamontology.org/format_1476
  - cmd: null
    input:
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        term: Protein interaction raw data
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      format:
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    note: null
    operation:
    - term: Peak calling
      uri: http://edamontology.org/operation_3222
    - term: Gene regulatory network analysis
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        uri: http://edamontology.org/data_1276
      format:
      - term: BED
        uri: http://edamontology.org/format_3003
  - cmd: null
    input:
    - data:
        term: Protein interaction raw data
        uri: http://edamontology.org/data_0905
      format:
      - term: FASTQ
        uri: http://edamontology.org/format_1930
    note: null
    operation:
    - term: Network analysis
      uri: http://edamontology.org/operation_3927
    - term: Nucleic acid folding analysis
      uri: http://edamontology.org/operation_0279
    output:
    - data:
        term: Topology data
        uri: http://edamontology.org/data_3872
      format:
      - term: pickle
        uri: http://edamontology.org/format_4002
    - data:
        term: Protein interaction data
        uri: http://edamontology.org/data_0906
      format:
      - term: pickle
        uri: http://edamontology.org/format_4002
  - cmd: null
    input:
    - data:
        term: Protein-ligand complex
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      format:
      - term: PDB
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    note: null
    operation:
    - term: Nucleic acid sequence analysis
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    output:
    - data:
        term: Nucleic acid report
        uri: http://edamontology.org/data_2084
      format: []
  - cmd: null
    input:
    - data:
        term: Structure
        uri: http://edamontology.org/data_0883
      format:
      - term: PDB
        uri: http://edamontology.org/format_1476
    note: null
    operation:
    - term: Molecular dynamics
      uri: http://edamontology.org/operation_2476
    - term: Nucleic acid structure analysis
      uri: http://edamontology.org/operation_2481
    output:
    - data:
        term: Trajectory data
        uri: http://edamontology.org/data_3870
      format: []
  - cmd: null
    input:
    - data:
        term: Protein interaction raw data
        uri: http://edamontology.org/data_0905
      format:
      - term: BAM
        uri: http://edamontology.org/format_2572
    note: null
    operation:
    - term: Nucleosome position prediction
      uri: http://edamontology.org/operation_0432
    - term: Phasing
      uri: http://edamontology.org/operation_3454
    output:
    - data:
        term: Annotation track
        uri: http://edamontology.org/data_3002
      format:
      - term: GFF
        uri: http://edamontology.org/format_2305
  - cmd: null
    input:
    - data:
        term: Sequence coordinates
        uri: http://edamontology.org/data_2012
      format: []
    - data:
        term: Annotation track
        uri: http://edamontology.org/data_3002
      format: []
    - data:
        term: Simulation
        uri: http://edamontology.org/data_3869
      format: []
    - data:
        term: Structure
        uri: http://edamontology.org/data_0883
      format: []
    note: null
    operation:
    - term: Visualisation
      uri: http://edamontology.org/operation_0337
    - term: Structure visualisation
      uri: http://edamontology.org/operation_0570
    - term: Sequence visualisation
      uri: http://edamontology.org/operation_0564
    - term: Network visualisation
      uri: http://edamontology.org/operation_3925
    output: []
  homepage: https://www.multiscalegenomics.eu/
  homepage_status: 0
  language:
  - PHP
  - Python
  lastUpdate: '2025-05-29T11:46:19.236621Z'
  license: Apache-2.0
  link:
  - note: null
    type:
    - Service
    url: http://vre.multiscalegenomics.eu
  - note: null
    type:
    - Repository
    url: https://github.com/Multiscale-Genomics/VRE
  maturity: null
  name: MuGVRE
  operatingSystem: []
  otherID: []
  owner: lcodo
  publication:
  - doi: 10.1101/602474
    metadata: null
    note: null
    pmcid: null
    pmid: null
    type:
    - Primary
    version: '1.0'
  relation:
  - biotoolsID: nucleosome_dynamics
    type: includes
  - biotoolsID: tadbit
    type: includes
  - biotoolsID: jbrowse
    type: includes
  - biotoolsID: ngl
    type: includes
  toolType:
  - Web application
  - Workbench
  topic:
  - term: DNA packaging
    uri: http://edamontology.org/topic_3176
  - term: ChIP-seq
    uri: http://edamontology.org/topic_3169
  - term: Nucleic acid structure analysis
    uri: http://edamontology.org/topic_0097
  - term: Molecular modelling
    uri: http://edamontology.org/topic_2275
  validated: 1
  version:
  - '1.0'
- accessibility: Open access
  additionDate: '2025-04-29T17:07:56.642694Z'
  biotoolsCURIE: biotools:biosurfdb
  biotoolsID: biosurfdb
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: jorge.oliveira@tecnico.ulisboa.pt
    fundrefid: null
    gridid: null
    name: Jorge S. Oliveira
    note: null
    orcidid: https://orcid.org/0000-0001-6425-2176
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: https://web.tecnico.ulisboa.pt/jorge.oliveira/
  - email: ana.freitas@tecnico.ulisboa.pt
    fundrefid: null
    gridid: null
    name: Ana Teresa Freitas
    note: null
    orcidid: http://orcid.org/0000-0003-4638-2879
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: null
  - email: atrv@lncc.br
    fundrefid: null
    gridid: null
    name: Ana Tereza Ribeiro de Vasconcelos
    note: null
    orcidid: http://orcid.org/0000-0002-4632-2086
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: null
  - email: lucymara.agnez@ufrn.br
    fundrefid: null
    gridid: null
    name: Lucymara Fassarella Agnez-Lima
    note: null
    orcidid: http://orcid.org/0000-0003-0642-3162
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: null
  - email: gpo@biodata.pt
    fundrefid: null
    gridid: null
    name: Gil Poiares-Oliveira
    note: null
    orcidid: https://orcid.org/0000-0003-4638-2879
    rorid: null
    typeEntity: Person
    typeRole:
    - Maintainer
    url: https://web.tecnico.ulisboa.pt/gil.oliveira
  description: BioSurfDB is a online database for biodegradation and biosurfactants.
  documentation: []
  download: []
  editPermission:
    authors:
    - gpo
    type: group
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: DNA sequence
        uri: http://edamontology.org/data_3494
      format: []
    - data:
        term: Protein sequence record
        uri: http://edamontology.org/data_2886
      format: []
    note: null
    operation:
    - term: Local alignment
      uri: http://edamontology.org/operation_0495
    output:
    - data:
        term: Nucleic acid sequence alignment
        uri: http://edamontology.org/data_1383
      format: []
    - data:
        term: Hybrid sequence alignment
        uri: http://edamontology.org/data_1385
      format: []
  - cmd: null
    input: []
    note: null
    operation:
    - term: Sequence database search (by property)
      uri: http://edamontology.org/operation_0349
    output:
    - data:
        term: Gene symbol
        uri: http://edamontology.org/data_1026
      format: []
    - data:
        term: Gene ID (NCBI)
        uri: http://edamontology.org/data_1027
      format: []
    - data:
        term: Gene name
        uri: http://edamontology.org/data_2299
      format: []
    - data:
        term: DNA sequence
        uri: http://edamontology.org/data_3494
      format: []
  homepage: https://www.biosurfdb.org
  homepage_status: 0
  language: []
  lastUpdate: '2025-04-29T17:35:41.655075Z'
  license: null
  link: []
  maturity: Mature
  name: BioSurfDB
  operatingSystem: []
  otherID: []
  owner: ELIXIR-PT
  publication:
  - doi: 10.1093/database/bav033
    metadata:
      abstract: 'Crude oil extraction, transportation and use provoke the contamination
        of countless ecosystems. Therefore, bioremediation through surfactants mobilization
        or biodegradation is an important subject, both economically and environmentally.
        Bioremediation research had a great boost with the recent advances in Metagenomics,
        as it enabled the sequencing of uncultured microorganisms providing new insights
        on surfactant-producing and/or oil-degrading bacteria. Many research studies
        are making available genomic data from unknown organisms obtained from metagenomics
        analysis of oil-contaminated environmental samples. These new datasets are
        presently demanding the development of new tools and data repositories tailored
        for the biological analysis in a context of bioremediation data analysis.
        This work presents BioSurfDB, www.biosurfdb.org, a curated relational information
        system integrating data from: (i) metagenomes; (ii) organisms; (iii) biodegradation
        relevant genes; proteins and their metabolic pathways; (iv) bioremediation
        experiments results, with specific pollutants treatment efficiencies by surfactant
        producing organisms; and (v) a biosurfactant-curated list, grouped by producing
        organism, surfactant name, class and reference. The main goal of this repository
        is to gather information on the characterization of biological compounds and
        mechanisms involved in biosurfactant production and/or biodegradation and
        make it available in a curated way and associated with a number of computational
        tools to support studies of genomic and metagenomic data.'
      authors:
      - name: Oliveira J.S.
      - name: Araujo W.
      - name: Sales A.I.L.
      - name: De Brito Guerra A.
      - name: Da Silva Araujo S.C.
      - name: De Vasconcelos A.T.R.
      - name: Agnez-Lima L.F.
      - name: Freitas A.T.
      citationCount: 30
      date: '2015-01-01T00:00:00Z'
      journal: Database
      title: 'BioSurfDB: Knowledge and algorithms to support biosurfactants and biodegradation
        studies'
    note: null
    pmcid: null
    pmid: null
    type:
    - Primary
    version: null
  relation: []
  toolType:
  - Database portal
  topic:
  - term: Biotechnology
    uri: http://edamontology.org/topic_3297
  - term: Microbiology
    uri: http://edamontology.org/topic_3301
  - term: Enzymes
    uri: http://edamontology.org/topic_0821
  validated: 0
  version: []
- accessibility: null
  additionDate: '2025-04-21T21:06:51.624399Z'
  biotoolsCURIE: biotools:samclip
  biotoolsID: samclip
  collectionID: []
  confidence_flag: null
  cost: null
  credit: []
  description: Filter SAM file for soft and hard clipped alignments
  documentation:
  - note: null
    type:
    - General
    url: https://github.com/tseemann/samclip
  download:
  - note: null
    type: Software package
    url: https://anaconda.org/bioconda/samclip
    version: 0.4.0
  editPermission:
    authors: []
    type: group
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  elixirNode: []
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  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Nucleic acid sequence alignment
        uri: http://edamontology.org/data_1383
      format: []
    note: null
    operation:
    - term: Sequence trimming
      uri: http://edamontology.org/operation_3192
    output:
    - data:
        term: Nucleic acid sequence alignment
        uri: http://edamontology.org/data_1383
      format: []
  homepage: https://github.com/tseemann/samclip
  homepage_status: 0
  language:
  - Perl
  lastUpdate: '2025-04-21T21:06:51.626575Z'
  license: null
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/tseemann/samclip
  maturity: null
  name: samclip
  operatingSystem:
  - Linux
  - Mac
  otherID: []
  owner: emmcauley
  publication: []
  relation: []
  toolType:
  - Command-line tool
  topic:
  - term: Genomics
    uri: http://edamontology.org/topic_0622
  - term: Bioinformatics
    uri: http://edamontology.org/topic_0091
  - term: Mapping
    uri: http://edamontology.org/topic_0102
  validated: 0
  version:
  - 0.4.0
- 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: '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
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        data. Here we exploited the long reads of the nanopore platform using our
        customized pipeline, Picky (https://github.com/TheJacksonLaboratory/Picky),
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        uncovered micro-insertions as the common structural features associated with
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      - name: Reyes A.
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      - name: Tenenbaum D.
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      - name: Morgan M.
      citationCount: 2315
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  description: A database designed to help the mycologist community to access to fungal
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        species barcodes or conserved sequences containing a high-quality phylogenetic
        signal. For the latter, identification relies on phylogenetic analyses and
        the adoption of the phylogenetic species concept. Such analysis requires that
        the reference sequences are well identified and deposited in public-access
        databases. However, many entries in the public sequence databases are problematic
        in terms of quality and reliability and these data require screening to ensure
        correct phylogenetic interpretation. Methods and Principal Findings: To facilitate
        phylogenetic inferences and phylogenetic assignment, we introduce a fungal
        sequence database. The database PHYMYCO-DB comprises fungal sequences from
        GenBank that have been filtered to satisfy stringent sequence quality criteria.
        For the first release, two widely used molecular taxonomic markers were chosen:
        the nuclear SSU rRNA and EF1-α gene sequences. Following the automatic extraction
        and filtration, a manual curation is performed to remove problematic sequences
        while preserving relevant sequences useful for phylogenetic studies. As a
        result of curation, ~20% of the automatically filtered sequences have been
        removed from the database. To demonstrate how PHYMYCO-DB can be employed,
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        sea samples. Conclusion: PHYMYCO-DB offers the tools necessary to: (i) extract
        high quality fungal sequences for each of the 5 fungal phyla, at all taxonomic
        levels, (ii) extract already performed alignments, to act as ''reference alignments'',
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        of 9120 SSU rRNA and 672 EF1-α high-quality fungal sequences are now available.
        The PHYMYCO-DB is accessible through the URL http://phymycodb.genouest.org.
        © 2012 Mahé et al.'
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      - name: Mahe S.
      - name: Duhamel M.
      - name: Le Calvez T.
      - name: Guillot L.
      - name: Sarbu L.
      - name: Bretaudeau A.
      - name: Collin O.
      - name: Dufresne A.
      - name: Kiers E.T.
      - name: Vandenkoornhuyse P.
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      journal: PLoS ONE
      title: 'PHYMYCO-DB: A Curated Database for Analyses of Fungal Diversity and
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      - name: Barton G.J.
      citationCount: 96
      date: '2011-07-01T00:00:00Z'
      journal: Bioinformatics
      title: Java bioinformatics analysis web services for multiple sequence alignment-JABAWS:MSA
    note: null
    pmcid: PMC3129525
    pmid: '21593132'
    type:
    - Review
    version: null
  relation: []
  toolType:
  - Web service
  topic:
  - term: Sequence analysis
    uri: http://edamontology.org/topic_0080
  validated: 1
  version:
  - '1'
- accessibility: null
  additionDate: '2017-01-17T14:57:43Z'
  biotoolsCURIE: biotools:rsamtools
  biotoolsID: rsamtools
  collectionID:
  - BioConductor
  - SAMtools utility
  confidence_flag: null
  cost: null
  credit:
  - email: maintainer@bioconductor.org
    fundrefid: null
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    name: BioConductor Package Maintainer
    note: null
    orcidid: null
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    typeEntity: Person
    typeRole:
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    url: null
  description: This package provides an interface to the 'samtools', 'bcftools', and
    'tabix' utilities (see 'LICENCE') for manipulating SAM (Sequence Alignment / Map),
    FASTA, binary variant call (BCF) and compressed indexed tab-delimited (tabix)
    files.
  documentation:
  - note: null
    type:
    - User manual
    url: http://bioconductor.org/packages/release/bioc/html/Rsamtools.html
  download:
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    input:
    - data:
        term: Sequence alignment (nucleic acid)
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      format:
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        uri: http://edamontology.org/format_2572
      - term: BCF
        uri: http://edamontology.org/format_3020
      - term: tabix
        uri: http://edamontology.org/format_3616
      - term: SAM
        uri: http://edamontology.org/format_2573
      - term: FASTA
        uri: http://edamontology.org/format_1929
    note: null
    operation:
    - term: Read pre-processing
      uri: http://edamontology.org/operation_3219
    - term: RNA-seq read count analysis
      uri: http://edamontology.org/operation_3563
    - term: Indexing
      uri: http://edamontology.org/operation_0227
    output:
    - data:
        term: Sequence alignment (nucleic acid)
        uri: http://edamontology.org/data_1383
      format:
      - term: BAI
        uri: http://edamontology.org/format_3327
    - data:
        term: Sequence coordinates
        uri: http://edamontology.org/data_2012
      format:
      - term: BAI
        uri: http://edamontology.org/format_3327
  homepage: http://bioconductor.org/packages/release/bioc/html/Rsamtools.html
  homepage_status: 0
  language:
  - R
  lastUpdate: '2024-11-25T14:17:52.982946Z'
  license: Artistic-2.0
  link:
  - note: null
    type:
    - Mirror
    url: http://bioconductor.org/packages/release/bioc/html/Rsamtools.html
  maturity: null
  name: Rsamtools
  operatingSystem:
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  - Mac
  otherID: []
  owner: bioconductor_import
  publication:
  - doi: 10.1038/nmeth.3252
    metadata:
      abstract: Bioconductor is an open-source, open-development software project
        for the analysis and comprehension of high-throughput data in genomics and
        molecular biology. The project aims to enable interdisciplinary research,
        collaboration and rapid development of scientific software. Based on the statistical
        programming language R, Bioconductor comprises 934 interoperable packages
        contributed by a large, diverse community of scientists. Packages cover a
        range of bioinformatic and statistical applications. They undergo formal initial
        review and continuous automated testing. We present an overview for prospective
        users and contributors.
      authors:
      - name: Huber W.
      - name: Carey V.J.
      - name: Gentleman R.
      - name: Anders S.
      - name: Carlson M.
      - name: Carvalho B.S.
      - name: Bravo H.C.
      - name: Davis S.
      - name: Gatto L.
      - name: Girke T.
      - name: Gottardo R.
      - name: Hahne F.
      - name: Hansen K.D.
      - name: Irizarry R.A.
      - name: Lawrence M.
      - name: Love M.I.
      - name: MaCdonald J.
      - name: Obenchain V.
      - name: Oles A.K.
      - name: Pages H.
      - name: Reyes A.
      - name: Shannon P.
      - name: Smyth G.K.
      - name: Tenenbaum D.
      - name: Waldron L.
      - name: Morgan M.
      citationCount: 2315
      date: '2015-01-01T00:00:00Z'
      journal: Nature Methods
      title: Orchestrating high-throughput genomic analysis with Bioconductor
    note: null
    pmcid: PMC4509590
    pmid: '25633503'
    type:
    - Other
    version: null
  relation: []
  toolType:
  - Command-line tool
  - Library
  topic:
  - term: RNA-Seq
    uri: http://edamontology.org/topic_3170
  validated: 1
  version:
  - 1.26.1
- accessibility: null
  additionDate: '2015-08-03T09:36:09Z'
  biotoolsCURIE: biotools:tcoffee
  biotoolsID: tcoffee
  collectionID:
  - T-Coffee
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: cedric.notredame@gmail.com
    fundrefid: null
    gridid: null
    name: Cedric Notredame
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: null
  description: A multiple sequence alignment package that can be used for DNA, RNA
    and protein sequences. It can be used to align sequences or to combine the output
    of other alignment methods (Clustal, Mafft, Probcons, Muscle...) into one unique
    alignment.
  documentation:
  - note: null
    type:
    - General
    url: http://www.tcoffee.org/Projects/tcoffee/
  - note: null
    type:
    - Installation instructions
    url: http://www.tcoffee.org/Projects/tcoffee/#INSTALLATION
  - note: T-Coffee README file
    type:
    - General
    url: http://www.tcoffee.org/Projects/tcoffee/documentation/README
  - note: null
    type:
    - FAQ
    url: http://www.tcoffee.org/Projects/tcoffee/#FAQ
  download:
  - note: null
    type: Downloads page
    url: http://www.tcoffee.org/Projects/tcoffee/#DOWNLOAD
    version: null
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  function:
  - cmd: null
    input:
    - data:
        term: Sequence
        uri: http://edamontology.org/data_2044
      format: []
    note: null
    operation:
    - term: Sequence analysis
      uri: http://edamontology.org/operation_2403
    - term: Multiple sequence alignment
      uri: http://edamontology.org/operation_0492
    output:
    - data:
        term: Sequence alignment
        uri: http://edamontology.org/data_0863
      format: []
  homepage: http://www.tcoffee.org/Projects/tcoffee/
  homepage_status: 0
  language: []
  lastUpdate: '2024-11-25T14:17:49.139161Z'
  license: GPL-3.0
  link:
  - note: null
    type:
    - Software catalogue
    url: https://www.biocatalogue.org/services/3720
  maturity: Mature
  name: T-Coffee
  operatingSystem:
  - Linux
  - Windows
  - Mac
  otherID: []
  owner: BioCatalogue
  publication:
  - doi: 10.1006/jmbi.2000.4042
    metadata:
      abstract: We describe a new method (T-Coffee) for multiple sequence alignment
        that provides a dramatic improvement in accuracy with a modest sacrifice in
        speed as compared to the most commonly used alternatives. The method is broadly
        based on the popular progressive approach to multiple alignment but avoids
        the most serious pitfalls caused by the greedy nature of this algorithm. With
        T-Coffee we pre-process a data set of all pair-wise alignments between the
        sequences. This provides us with a library of alignment information that can
        be used to guide the progressive alignment. Intermediate alignments are then
        based not only on the sequences to be aligned next but also on how all of
        the sequences align with each other. This alignment information can be derived
        from heterogeneous sources such as a mixture of alignment programs and/or
        structure superposition. Here, we illustrate the power of the approach by
        using a combination of local and global pair-wise alignments to generate the
        library. The resulting alignments are significantly more reliable, as determined
        by comparison with a set of 141 test cases, than any of the popular alternatives
        that we tried. The improvement, especially clear with the more difficult test
        cases, is always visible, regardless of the phylogenetic spread of the sequences
        in the tests. (C) 2000 Academic Press.
      authors:
      - name: Notredame C.
      - name: Higgins D.G.
      - name: Heringa J.
      citationCount: 5803
      date: '2000-09-08T00:00:00Z'
      journal: Journal of Molecular Biology
      title: 'T-coffee: A novel method for fast and accurate multiple sequence alignment'
    note: null
    pmcid: null
    pmid: '10964570'
    type:
    - Primary
    version: null
  relation: []
  toolType:
  - Command-line tool
  topic:
  - term: Sequence analysis
    uri: http://edamontology.org/topic_0080
  validated: 1
  version:
  - '1'
- accessibility: null
  additionDate: '2015-08-03T09:36:10Z'
  biotoolsCURIE: biotools:muscle_ws_jabaws
  biotoolsID: muscle_ws_jabaws
  collectionID:
  - MUSCLE
  - JABAWS
  confidence_flag: null
  cost: null
  credit:
  - email: null
    fundrefid: null
    gridid: null
    name: BioCatalogue
    note: null
    orcidid: null
    rorid: null
    typeEntity: Project
    typeRole:
    - Documentor
    url: https://www.biocatalogue.org
  - email: null
    fundrefid: null
    gridid: null
    name: null
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: http://www.compbio.dundee.ac.uk/jabaws/contacts.html
  description: Multiple sequence algnment tool.
  documentation:
  - note: null
    type:
    - User manual
    url: http://www.compbio.dundee.ac.uk/jabaws/man_about.html
  - note: null
    type:
    - API documentation
    url: http://www.compbio.dundee.ac.uk/jabaws/full_javadoc/compbio/ws/server/MuscleWS.html
  download: []
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  function:
  - cmd: null
    input:
    - data:
        term: Sequence
        uri: http://edamontology.org/data_2044
      format: []
    note: null
    operation:
    - term: Multiple sequence alignment
      uri: http://edamontology.org/operation_0492
    output:
    - data:
        term: Sequence alignment
        uri: http://edamontology.org/data_0863
      format: []
  homepage: http://www.compbio.dundee.ac.uk/jabaws
  homepage_status: 0
  language:
  - Java
  lastUpdate: '2024-11-25T14:17:47.947650Z'
  license: null
  link:
  - note: null
    type:
    - Software catalogue
    url: https://www.biocatalogue.org/services/3759
  maturity: null
  name: Muscle WS (jabaws)
  operatingSystem:
  - Linux
  - Windows
  - Mac
  otherID: []
  owner: BioCatalogue
  publication:
  - doi: 10.1093/bioinformatics/btr304
    metadata:
      abstract: 'Summary: JABAWS is a web services framework that simplifies the deployment
        of web services for bioinformatics. JABAWS:MSA provides services for five
        multiple sequence alignment (MSA) methods (Probcons, T-coffee, Muscle, Mafft
        and ClustalW), and is the system employed by the Jalview multiple sequence
        analysis workbench since version 2.6. A fully functional, easy to set up server
        is provided as a Virtual Appliance (VA), which can be run on most operating
        systems that support a virtualization environment such as VMware or Oracle
        VirtualBox. JABAWS is also distributed as a Web Application aRchive (WAR)
        and can be configured to run on a single computer and/or a cluster managed
        by Grid Engine, LSF or other queuing systems that support DRMAA. JABAWS:MSA
        provides clients full access to each application''s parameters, allows administrators
        to specify named parameter preset combinations and execution limits for each
        application through simple configuration files. The JABAWS command-line client
        allows integration of JABAWS services into conventional scripts. © The Author(s)
        2011. Published by Oxford University Press.'
      authors:
      - name: Troshin P.V.
      - name: Procter J.B.
      - name: Barton G.J.
      citationCount: 96
      date: '2011-07-01T00:00:00Z'
      journal: Bioinformatics
      title: Java bioinformatics analysis web services for multiple sequence alignment-JABAWS:MSA
    note: null
    pmcid: PMC3129525
    pmid: '21593132'
    type:
    - Review
    version: null
  relation: []
  toolType:
  - Web service
  topic:
  - term: Sequence analysis
    uri: http://edamontology.org/topic_0080
  validated: 1
  version:
  - '1'
- accessibility: null
  additionDate: '2017-01-13T13:13:56Z'
  biotoolsCURIE: biotools:bwa
  biotoolsID: bwa
  collectionID:
  - BWA
  confidence_flag: null
  cost: null
  credit:
  - email: bio-bwa-help@sourceforge.net
    fundrefid: null
    gridid: null
    name: bwa team
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: null
  - email: me@liheng.org
    fundrefid: null
    gridid: null
    name: Heng Li
    note: null
    orcidid: http://orcid.org/0000-0003-4874-2874
    rorid: null
    typeEntity: Person
    typeRole:
    - Contributor
    url: http://www.liheng.org/
  description: Fast, accurate, memory-efficient aligner for short and long sequencing
    reads
  documentation:
  - note: null
    type:
    - User manual
    url: http://bio-bwa.sourceforge.net/bwa.shtml
  download:
  - note: null
    type: Tool wrapper (CWL)
    url: https://gitlab.com/sibyllewohlgemuth/cwl_files/raw/master/bwa_index.cwl
    version: null
  - note: null
    type: Tool wrapper (CWL)
    url: https://gitlab.com/sibyllewohlgemuth/cwl_files/raw/master/bwa_mem.cwl
    version: null
  - note: null
    type: Container file
    url: https://docker-ui.genouest.org/app/#/container/bioconda/bwa
    version: null
  - note: null
    type: Container file
    url: https://anaconda.org/bioconda/bwa
    version: null
  editPermission:
    authors:
    - swohlgemuth
    type: group
  elixirCommunity: []
  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: Index database sequences in the FASTA format. database
    operation:
    - term: Genome indexing
      uri: http://edamontology.org/operation_3211
    output:
    - data:
        term: Genome index
        uri: http://edamontology.org/data_3210
      format: []
  - cmd: null
    input:
    - data:
        term: Genome index
        uri: http://edamontology.org/data_3210
      format: []
    - data:
        term: Sequence
        uri: http://edamontology.org/data_2044
      format:
      - term: FASTQ
        uri: http://edamontology.org/format_1930
    note: Align 70bp-1Mbp query sequences with the BWA-MEM algorithm. Briefly, the
      algorithm works by seeding alignments with maximal exact matches (MEMs) and
      then extending seeds with the affine-gap Smith-Waterman algorithm (SW). The
      BWA-MEM algorithm performs local alignment. It may produce multiple primary
      alignments for different part of a query sequence. This is a crucial feature
      for long sequences. However, some tools such as Picards markDuplicates does
      not work with split alignments. One may consider to use option -M to flag shorter
      split hits as secondary.
    operation:
    - term: Sequence alignment
      uri: http://edamontology.org/operation_0292
    output:
    - data:
        term: Alignment
        uri: http://edamontology.org/data_1916
      format: []
  - cmd: null
    input:
    - data:
        term: Sequence
        uri: http://edamontology.org/data_2044
      format:
      - term: FASTA search results format
        uri: http://edamontology.org/format_1332
    - data:
        term: Sequence
        uri: http://edamontology.org/data_2044
      format:
      - term: FASTQ
        uri: http://edamontology.org/format_1930
    note: Find the SA coordinates of the input reads. reference sequence query sequence
    operation:
    - term: Read mapping
      uri: http://edamontology.org/operation_3198
    - term: Sequence alignment
      uri: http://edamontology.org/operation_0292
    output:
    - data:
        term: Sequence coordinates
        uri: http://edamontology.org/data_2012
      format: []
  - 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: FASTQ
        uri: http://edamontology.org/format_1930
    - data:
        term: Sequence
        uri: http://edamontology.org/data_2044
      format: []
    note: Generate alignments in the SAM format given single-end reads. Repetitive
      hits will be randomly chosen reference sequence query sequence
    operation:
    - term: Generation
      uri: http://edamontology.org/operation_3429
    - term: Sequence alignment
      uri: http://edamontology.org/operation_0292
    output:
    - data:
        term: Sequence alignment
        uri: http://edamontology.org/data_0863
      format:
      - term: SAM
        uri: http://edamontology.org/format_2573
  - 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: []
    - data:
        term: Sequence
        uri: http://edamontology.org/data_2044
      format:
      - term: FASTQ
        uri: http://edamontology.org/format_1930
    note: Generate alignments in the SAM format given paired-end reads. Repetitive
      read pairs will be placed randomly. reference sequence
    operation:
    - term: Generation
      uri: http://edamontology.org/operation_3429
    - term: Sequence alignment
      uri: http://edamontology.org/operation_0292
    output:
    - data:
        term: Sequence alignment
        uri: http://edamontology.org/data_0863
      format:
      - term: SAM
        uri: http://edamontology.org/format_2573
  - 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: FASTQ
        uri: http://edamontology.org/format_1930
    note: Align query sequences in the in.fq file reference sequence
    operation:
    - term: Sequence alignment
      uri: http://edamontology.org/operation_0292
    output:
    - data:
        term: Sequence alignment
        uri: http://edamontology.org/data_0863
      format: []
  homepage: http://bio-bwa.sourceforge.net
  homepage_status: 0
  language:
  - C
  lastUpdate: '2024-11-25T14:09:49.679089Z'
  license: MIT
  link: []
  maturity: Mature
  name: BWA
  operatingSystem:
  - Linux
  - Mac
  otherID: []
  owner: seqwiki_import
  publication:
  - doi: 10.1093/bioinformatics/btp324
    metadata:
      abstract: 'Motivation: The enormous amount of short reads generated by the new
        DNA sequencing technologies call for the development of fast and accurate
        read alignment programs. A first generation of hash table-based methods has
        been developed, including MAQ, which is accurate, feature rich and fast enough
        to align short reads from a single individual. However, MAQ does not support
        gapped alignment for single-end reads, which makes it unsuitable for alignment
        of longer reads where indels may occur frequently. The speed of MAQ is also
        a concern when the alignment is scaled up to the resequencing of hundreds
        of individuals. Results: We implemented Burrows-Wheeler Alignment tool (BWA),
        a new read alignment package that is based on backward search with Burrows-Wheeler
        Transform (BWT), to efficiently align short sequencing reads against a large
        reference sequence such as the human genome, allowing mismatches and gaps.
        BWA supports both base space reads, e.g. from Illumina sequencing machines,
        and color space reads from AB SOLiD machines. Evaluations on both simulated
        and real data suggest that BWA is ∼10-20× faster than MAQ, while achieving
        similar accuracy. In addition, BWA outputs alignment in the new standard SAM
        (Sequence Alignment/Map) format. Variant calling and other downstream analyses
        after the alignment can be achieved with the open source SAMtools software
        package. © 2009 The Author(s).'
      authors:
      - name: Li H.
      - name: Durbin R.
      citationCount: 33667
      date: '2009-07-01T00:00:00Z'
      journal: Bioinformatics
      title: Fast and accurate short read alignment with Burrows-Wheeler transform
    note: null
    pmcid: PMC2705234
    pmid: '19451168'
    type:
    - Primary
    version: null
  - doi: 10.1186/1471-2105-14-184
    metadata:
      abstract: 'Background: The development of next-generation sequencing instruments
        has led to the generation of millions of short sequences in a single run.
        The process of aligning these reads to a reference genome is time consuming
        and demands the development of fast and accurate alignment tools. However,
        the current proposed tools make different compromises between the accuracy
        and the speed of mapping. Moreover, many important aspects are overlooked
        while comparing the performance of a newly developed tool to the state of
        the art. Therefore, there is a need for an objective evaluation method that
        covers all the aspects. In this work, we introduce a benchmarking suite to
        extensively analyze sequencing tools with respect to various aspects and provide
        an objective comparison.Results: We applied our benchmarking tests on 9 well
        known mapping tools, namely, Bowtie, Bowtie2, BWA, SOAP2, MAQ, RMAP, GSNAP,
        Novoalign, and mrsFAST (mrFAST) using synthetic data and real RNA-Seq data.
        MAQ and RMAP are based on building hash tables for the reads, whereas the
        remaining tools are based on indexing the reference genome. The benchmarking
        tests reveal the strengths and weaknesses of each tool. The results show that
        no single tool outperforms all others in all metrics. However, Bowtie maintained
        the best throughput for most of the tests while BWA performed better for longer
        read lengths. The benchmarking tests are not restricted to the mentioned tools
        and can be further applied to others.Conclusion: The mapping process is still
        a hard problem that is affected by many factors. In this work, we provided
        a benchmarking suite that reveals and evaluates the different factors affecting
        the mapping process. Still, there is no tool that outperforms all of the others
        in all the tests. Therefore, the end user should clearly specify his needs
        in order to choose the tool that provides the best results. © 2013 Hatem et
        al.; licensee BioMed Central Ltd.'
      authors:
      - name: Hatem A.
      - name: Bozdag D.
      - name: Toland A.E.
      - name: Catalyurek U.V.
      citationCount: 146
      date: '2013-06-07T00:00:00Z'
      journal: BMC Bioinformatics
      title: Benchmarking short sequence mapping tools
    note: null
    pmcid: PMC3694458
    pmid: '23758764'
    type:
    - Benchmarking study
    version: null
  - doi: 10.1016/j.ygeno.2017.03.001
    metadata:
      abstract: Massive data produced due to the advent of next-generation sequencing
        (NGS) technology is widely used for biological researches and medical diagnosis.
        The crucial step in NGS analysis is read alignment or mapping which is computationally
        intensive and complex. The mapping bias tends to affect the downstream analysis,
        including detection of polymorphisms. In order to provide guidelines to the
        biologist for suitable selection of aligners; we have evaluated and benchmarked
        5 different aligners (BWA, Bowtie2, NovoAlign, Smalt and Stampy) and their
        mapping bias based on characteristics of 5 microbial genomes. Two million
        simulated read pairs of various sizes (36 bp, 50 bp, 72 bp, 100 bp, 125 bp,
        150 bp, 200 bp, 250 bp and 300 bp) were aligned. Specific alignment features
        such as sensitivity of mapping, percentage of properly paired reads, alignment
        time and effect of tandem repeats on incorrectly mapped reads were evaluated.
        BWA showed faster alignment followed by Bowtie2 and Smalt. NovoAlign and Stampy
        were comparatively slower. Most of the aligners showed high sensitivity towards
        long reads (> 100 bp) mapping. On the other hand NovoAlign showed higher sensitivity
        towards both short reads (36 bp, 50 bp, 72 bp) and long reads (> 100 bp) mappings;
        It also showed higher sensitivity towards mapping a complex genome like Plasmodium
        falciparum. The percentage of properly paired reads aligned by NovoAlign,
        BWA and Stampy were markedly higher. None of the aligners outperforms the
        others in the benchmark, however the aligners perform differently with genome
        characteristics. We expect that the results from this study will be useful
        for the end user to choose aligner, thus enhance the accuracy of read mapping.
      authors:
      - name: Thankaswamy-Kosalai S.
      - name: Sen P.
      - name: Nookaew I.
      citationCount: 54
      date: '2017-07-01T00:00:00Z'
      journal: Genomics
      title: Evaluation and assessment of read-mapping by multiple next-generation
        sequencing aligners based on genome-wide characteristics
    note: null
    pmcid: null
    pmid: '28286147'
    type: []
    version: null
  - doi: 10.1186/1471-2164-15-264
    metadata:
      abstract: 'Background: The rapid evolution in high-throughput sequencing (HTS)
        technologies has opened up new perspectives in several research fields and
        led to the production of large volumes of sequence data. A fundamental step
        in HTS data analysis is the mapping of reads onto reference sequences. Choosing
        a suitable mapper for a given technology and a given application is a subtle
        task because of the difficulty of evaluating mapping algorithms.Results: In
        this paper, we present a benchmark procedure to compare mapping algorithms
        used in HTS using both real and simulated datasets and considering four evaluation
        criteria: computational resource and time requirements, robustness of mapping,
        ability to report positions for reads in repetitive regions, and ability to
        retrieve true genetic variation positions. To measure robustness, we introduced
        a new definition for a correctly mapped read taking into account not only
        the expected start position of the read but also the end position and the
        number of indels and substitutions. We developed CuReSim, a new read simulator,
        that is able to generate customized benchmark data for any kind of HTS technology
        by adjusting parameters to the error types. CuReSim and CuReSimEval, a tool
        to evaluate the mapping quality of the CuReSim simulated reads, are freely
        available. We applied our benchmark procedure to evaluate 14 mappers in the
        context of whole genome sequencing of small genomes with Ion Torrent data
        for which such a comparison has not yet been established.Conclusions: A benchmark
        procedure to compare HTS data mappers is introduced with a new definition
        for the mapping correctness as well as tools to generate simulated reads and
        evaluate mapping quality. The application of this procedure to Ion Torrent
        data from the whole genome sequencing of small genomes has allowed us to validate
        our benchmark procedure and demonstrate that it is helpful for selecting a
        mapper based on the intended application, questions to be addressed, and the
        technology used. This benchmark procedure can be used to evaluate existing
        or in-development mappers as well as to optimize parameters of a chosen mapper
        for any application and any sequencing platform. © 2014 Caboche et al.; licensee
        BioMed Central Ltd.'
      authors:
      - name: Caboche S.
      - name: Audebert C.
      - name: Lemoine Y.
      - name: Hot D.
      citationCount: 66
      date: '2014-04-05T00:00:00Z'
      journal: BMC Genomics
      title: 'Comparison of mapping algorithms used in high-throughput sequencing:
        Application to Ion Torrent data'
    note: null
    pmcid: PMC4051166
    pmid: '24708189'
    type:
    - Benchmarking study
    version: null
  - doi: 10.1093/bioinformatics/btu146
    metadata:
      abstract: 'Motivation: Next-generation sequencing has become an important tool
        in molecular biology. Various protocols to investigate genomic, transcriptomic
        and epigenomic features across virtually all species and tissues have been
        devised. For most of these experiments, one of the first crucial steps of
        bioinformatic analysis is the mapping of reads to reference genomes. Results:
        Here, we present thorough benchmarks of our read aligner segemehl in comparison
        with other state-of-the-art methods. Furthermore, we introduce the tool lack
        to rescue unmapped RNA-seq reads which works in conjunction with segemehl
        and many other frequently used split-read aligners. © The Author 2014.'
      authors:
      - name: Otto C.
      - name: Stadler P.F.
      - name: Hoffmann S.
      citationCount: 71
      date: '2014-07-01T00:00:00Z'
      journal: Bioinformatics
      title: Lacking alignments? The next-generation sequencing mapper segemehl revisited
    note: null
    pmcid: null
    pmid: '24626854'
    type: []
    version: null
  - doi: 10.1093/bioinformatics/btp698
    metadata:
      abstract: 'Motivation: Many programs for aligning short sequencing reads to
        a reference genome have been developed in the last 2 years. Most of them are
        very efficient for short reads but inefficient or not applicable for reads
        >200 bp because the algorithms are heavily and specifically tuned for short
        queries with low sequencing error rate. However, some sequencing platforms
        already produce longer reads and others are expected to become available soon.
        For longer reads, hashingbased software such as BLAT and SSAHA2 remain the
        only choices. Nonetheless, these methods are substantially slower than short-read
        aligners in terms of aligned bases per unit time. Results: We designed and
        implemented a new algorithm, Burrows-Wheeler Aligner''s Smith-Waterman Alignment
        (BWA-SW), to align long sequences up to 1Mb against a large sequence database
        (e.g. the human genome) with a few gigabytes of memory. The algorithm is as
        accurate as SSAHA2, more accurate than BLAT, and is several to tens of times
        faster than both. Availability: http://bio-bwa.sourceforge.net. Contact: rd@sanger.ac.uk
        © The Author(s) 2010. Published by Oxford University Press.'
      authors:
      - name: Li H.
      - name: Durbin R.
      citationCount: 8584
      date: '2010-01-15T00:00:00Z'
      journal: Bioinformatics
      title: Fast and accurate long-read alignment with Burrows-Wheeler transform
    note: null
    pmcid: PMC2828108
    pmid: '20080505'
    type: []
    version: null
  relation: []
  toolType:
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  - Workbench
  topic:
  - term: Mapping
    uri: http://edamontology.org/topic_0102
  validated: 1
  version: []
- accessibility: null
  additionDate: '2016-04-22T09:22:48Z'
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    name: Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben
    note: null
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    rorid: null
    typeEntity: Institute
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    url: null
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    note: null
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    typeEntity: Institute
    typeRole:
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    url: null
  - email: scholz@ipk-gatersleben.de
    fundrefid: null
    gridid: null
    name: Dr. Uwe Scholz
    note: null
    orcidid: null
    rorid: null
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    typeRole:
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    url: null
  - email: scholz@ipk-gatersleben.de
    fundrefid: null
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    name: Dr. Uwe Scholz
    note: null
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    rorid: null
    typeEntity: Person
    typeRole:
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    url: null
  description: A homology search against the current barley sequences resources is
    provided. The complete sequences data set comprises the whole genome shotgun assemblies
    of the cultivars Morex, Barke and Bowman as well as the high and low confidence
    gene sets. The newest POPSEQ anchoring data is integrated. Furthermore, the barley
    exome capture targets are provided. Additionally, resources like bacterial artificial
    chromosome assemblies, BAC end sequences and full length cDNAs are included.
  documentation:
  - note: null
    type:
    - Citation instructions
    url: http://dx.doi.org/10.3835/plantgenome2015.06.0038
  - note: null
    type:
    - General
    url: http://webblast.ipk-gatersleben.de/barley_ibsc/docs/blast_databases.html
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    type:
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    input:
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    note: null
    operation:
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      uri: http://edamontology.org/operation_0346
    output:
    - data:
        term: Sequence alignment
        uri: http://edamontology.org/data_0863
      format:
      - term: Alignment format
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  homepage: http://webblast.ipk-gatersleben.de
  homepage_status: 0
  language:
  - Java
  lastUpdate: '2024-11-25T14:07:20.696381Z'
  license: null
  link: []
  maturity: null
  name: IPK BLAST Server
  operatingSystem:
  - Linux
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  owner: ipk
  publication:
  - doi: 10.3835/plantgenome2015.06.0038
    metadata:
      abstract: The genome sequences of many important Triticeae species, including
        bread wheat (Triticum aestivum L.) and barley (Hordeum vulgare L.), remained
        uncharacterized for a long time because their high repeat content, large sizes,
        and polyploidy. As a result of improvements in sequencing technologies and
        novel analyses strategies, several of these have recently been deciphered.
        These efforts have generated new insights into Triticeae biology and genome
        organization and have important implications for downstream usage by breeders,
        experimental biologists, and comparative genomicists. transPLANT (http://www.transplantdb.eu)
        is an EU-funded project aimed at constructing hardware, software, and data
        infrastructure for genome-scale research in the life sciences. Since the Triticeae
        data are intrinsically complex, heterogenous, and distributed, the transPLANT
        consortium has undertaken efforts to develop common data formats and tools
        that enable the exchange and integration of data from distributed resources.
        Here we present an overview of the individual Triticeae genome resources hosted
        by transPLANT partners, introduce the objectives of transPLANT, and outline
        common developments and interfaces supporting integrated data access.
      authors:
      - name: Spannagl M.
      - name: Alaux M.
      - name: Lange M.
      - name: Bolser D.M.
      - name: Bader K.C.
      - name: Letellier T.
      - name: Kimmel E.
      - name: Flores R.
      - name: Pommier C.
      - name: Kerhornou A.
      - name: Walts B.
      - name: Nussbaumer T.
      - name: Grabmuller C.
      - name: Chen J.
      - name: Colmsee C.
      - name: Beier S.
      - name: Mascher M.
      - name: Schmutzer T.
      - name: Arend D.
      - name: Thanki A.
      - name: Ramirez-Gonzalez R.
      - name: Ayling M.
      - name: Ayling S.
      - name: Caccamo M.
      - name: Mayer K.F.X.
      - name: Scholz U.
      - name: Steinbach D.
      - name: Quesneville H.
      - name: Kersey P.J.
      citationCount: 6
      date: '2016-03-01T00:00:00Z'
      journal: Plant Genome
      title: TransPLANT resources for triticeae genomic data
    note: null
    pmcid: null
    pmid: '27898761'
    type:
    - Primary
    version: null
  relation:
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  toolType:
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  topic:
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    uri: http://edamontology.org/topic_3053
  validated: 1
  version:
  - '1'
- accessibility: null
  additionDate: '2015-01-29T15:47:59Z'
  biotoolsCURIE: biotools:ensembl_genomes_metazoa_blast
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  - EBI Tools
  confidence_flag: null
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    typeRole:
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    url: null
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    name: EMBL-EBI
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    typeEntity: Institute
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    url: null
  - email: helpdesk@ensemblgenomes.org
    fundrefid: null
    gridid: null
    name: null
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    rorid: null
    typeEntity: Person
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  - email: eg-webteam@ebi.ac.uk
    fundrefid: null
    gridid: null
    name: Ensembl Genomes webteam
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
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    url: null
  description: Searches Ensembl Metazoa sequences using Exonerate.
  documentation:
  - note: null
    type:
    - Terms of use
    url: http://www.ebi.ac.uk/about/terms-of-use
  - note: null
    type:
    - General
    url: http://metazoa.ensembl.org/info/website/help/index.html
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  function:
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    input:
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      format:
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        uri: http://edamontology.org/format_1929
    note: null
    operation:
    - term: Sequence similarity search
      uri: http://edamontology.org/operation_0346
    output:
    - data:
        term: Sequence alignment
        uri: http://edamontology.org/data_0863
      format: []
    - data:
        term: Sequence search results
        uri: http://edamontology.org/data_0857
      format: []
  homepage: http://metazoa.ensembl.org/Multi/blastview
  homepage_status: 0
  language: []
  lastUpdate: '2024-11-25T14:07:17.756843Z'
  license: null
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  name: Ensembl Genomes Metazoa Blast
  operatingSystem:
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  - Windows
  - Mac
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  owner: EMBL-EBI
  publication:
  - doi: 10.1093/nar/gkv1157
    metadata:
      abstract: The Ensembl project (http://www.ensembl.org) is a system for genome
        annotation, analysis, storage and dissemination designed to facilitate the
        access of genomic annotation from chordates and key model organisms. It provides
        access to data from 87 species across our main and early access Pre! websites.
        This year we introduced three newly annotated species and released numerous
        updates across our supported species with a concentration on data for the
        latest genome assemblies of human, mouse, zebrafish and rat. We also provided
        two data updates for the previous human assembly, GRCh37, through a dedicated
        website (http://grch37.ensembl.org). Our tools, in particular the VEP, have
        been improved significantly through integration of additional third party
        data. REST is now capable of larger-scale analysis and our regulatory data
        BioMart can deliver faster results. The website is now capable of displaying
        long-range interactions such as those found in cis-regulated datasets. Finally
        we have launched a website optimized for mobile devices providing views of
        genes, variants and phenotypes. Our data is made available without restriction
        and all code is available from our GitHub organization site (http://github.com/Ensembl)
        under an Apache 2.0 license.
      authors:
      - name: Yates A.
      - name: Akanni W.
      - name: Amode M.R.
      - name: Barrell D.
      - name: Billis K.
      - name: Carvalho-Silva D.
      - name: Cummins C.
      - name: Clapham P.
      - name: Fitzgerald S.
      - name: Gil L.
      - name: Giron C.G.
      - name: Gordon L.
      - name: Hourlier T.
      - name: Hunt S.E.
      - name: Janacek S.H.
      - name: Johnson N.
      - name: Juettemann T.
      - name: Keenan S.
      - name: Lavidas I.
      - name: Martin F.J.
      - name: Maurel T.
      - name: McLaren W.
      - name: Murphy D.N.
      - name: Nag R.
      - name: Nuhn M.
      - name: Parker A.
      - name: Patricio M.
      - name: Pignatelli M.
      - name: Rahtz M.
      - name: Riat H.S.
      - name: Sheppard D.
      - name: Taylor K.
      - name: Thormann A.
      - name: Vullo A.
      - name: Wilder S.P.
      - name: Zadissa A.
      - name: Birney E.
      - name: Harrow J.
      - name: Muffato M.
      - name: Perry E.
      - name: Ruffier M.
      - name: Spudich G.
      - name: Trevanion S.J.
      - name: Cunningham F.
      - name: Aken B.L.
      - name: Zerbino D.R.
      - name: Flicek P.
      citationCount: 1097
      date: '2016-01-01T00:00:00Z'
      journal: Nucleic Acids Research
      title: Ensembl 2016
    note: null
    pmcid: PMC4702834
    pmid: '26687719'
    type:
    - Other
    version: null
  relation:
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  toolType:
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  topic:
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    uri: http://edamontology.org/topic_0080
  validated: 0
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- accessibility: null
  additionDate: '2015-01-29T15:47:59Z'
  biotoolsCURIE: biotools:ensembl_genomes_plants_blast
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    typeRole:
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  - email: eg-webteam@ebi.ac.uk
    fundrefid: null
    gridid: null
    name: Ensembl Genomes webteam
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
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    url: null
  description: Search Ensembl Plants sequences with WU-BLAST.
  documentation:
  - note: null
    type:
    - Terms of use
    url: http://www.ebi.ac.uk/about/terms-of-use
  - note: null
    type:
    - General
    url: http://plants.ensembl.org/info/website/help/index.html
  download: []
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  function:
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    input:
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    note: null
    operation:
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    output:
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      format: []
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  name: Ensembl Genomes Plants Blast
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    metadata:
      abstract: The Ensembl project (http://www.ensembl.org) is a system for genome
        annotation, analysis, storage and dissemination designed to facilitate the
        access of genomic annotation from chordates and key model organisms. It provides
        access to data from 87 species across our main and early access Pre! websites.
        This year we introduced three newly annotated species and released numerous
        updates across our supported species with a concentration on data for the
        latest genome assemblies of human, mouse, zebrafish and rat. We also provided
        two data updates for the previous human assembly, GRCh37, through a dedicated
        website (http://grch37.ensembl.org). Our tools, in particular the VEP, have
        been improved significantly through integration of additional third party
        data. REST is now capable of larger-scale analysis and our regulatory data
        BioMart can deliver faster results. The website is now capable of displaying
        long-range interactions such as those found in cis-regulated datasets. Finally
        we have launched a website optimized for mobile devices providing views of
        genes, variants and phenotypes. Our data is made available without restriction
        and all code is available from our GitHub organization site (http://github.com/Ensembl)
        under an Apache 2.0 license.
      authors:
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      - name: Akanni W.
      - name: Amode M.R.
      - name: Barrell D.
      - name: Billis K.
      - name: Carvalho-Silva D.
      - name: Cummins C.
      - name: Clapham P.
      - name: Fitzgerald S.
      - name: Gil L.
      - name: Giron C.G.
      - name: Gordon L.
      - name: Hourlier T.
      - name: Hunt S.E.
      - name: Janacek S.H.
      - name: Johnson N.
      - name: Juettemann T.
      - name: Keenan S.
      - name: Lavidas I.
      - name: Martin F.J.
      - name: Maurel T.
      - name: McLaren W.
      - name: Murphy D.N.
      - name: Nag R.
      - name: Nuhn M.
      - name: Parker A.
      - name: Patricio M.
      - name: Pignatelli M.
      - name: Rahtz M.
      - name: Riat H.S.
      - name: Sheppard D.
      - name: Taylor K.
      - name: Thormann A.
      - name: Vullo A.
      - name: Wilder S.P.
      - name: Zadissa A.
      - name: Birney E.
      - name: Harrow J.
      - name: Muffato M.
      - name: Perry E.
      - name: Ruffier M.
      - name: Spudich G.
      - name: Trevanion S.J.
      - name: Cunningham F.
      - name: Aken B.L.
      - name: Zerbino D.R.
      - name: Flicek P.
      citationCount: 1097
      date: '2016-01-01T00:00:00Z'
      journal: Nucleic Acids Research
      title: Ensembl 2016
    note: null
    pmcid: PMC4702834
    pmid: '26687719'
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    version: null
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- accessibility: null
  additionDate: '2015-07-28T11:14:46Z'
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  description: Easy-to-use webserver that makes it possible to simultaneously use
    the best methods for aligning and predicting the consensus secondary structure
    for a set of non-coding RNA sequences.
  documentation:
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  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: RNA sequence
        uri: http://edamontology.org/data_3495
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
    - data:
        term: Sequence alignment
        uri: http://edamontology.org/data_0863
      format:
      - term: Stockholm format
        uri: http://edamontology.org/format_1961
    note: null
    operation:
    - term: RNA secondary structure prediction
      uri: http://edamontology.org/operation_0278
    - term: Sequence alignment
      uri: http://edamontology.org/operation_0292
    output:
    - data:
        term: Sequence alignment
        uri: http://edamontology.org/data_0863
      format:
      - term: ClustalW format
        uri: http://edamontology.org/format_1982
      - term: Stockholm format
        uri: http://edamontology.org/format_1961
      - term: FASTA
        uri: http://edamontology.org/format_1929
  homepage: http://genome.ku.dk/resources/war/
  homepage_status: 0
  language: []
  lastUpdate: '2024-11-25T14:06:15.464725Z'
  license: null
  link: []
  maturity: null
  name: WAR
  operatingSystem:
  - Linux
  - Windows
  - Mac
  otherID: []
  owner: admin
  publication:
  - doi: 10.1093/nar/gkn275
    metadata:
      abstract: 'We present an easy-to-use webserver that makes it possible to simultaneously
        use a number of state of the art methods for performing multiple alignment
        and secondary structure prediction for noncoding RNA sequences. This makes
        it possible to use the programs without having to download the code and get
        the programs to run. The results of all the programs are presented on a webpage
        and can easily be downloaded for further analysis. Additional measures are
        calculated for each program to make it easier to judge the individual predictions,
        and a consensus prediction taking all the programs into account is also calculated.
        This website is free and open to all users and there is no login requirement.
        The webserver can be found at: http://genome.ku.dk/resources/war.'
      authors:
      - name: Torarinsson E.
      - name: Lindgreen S.
      citationCount: 41
      date: '2008-01-01T00:00:00Z'
      journal: Nucleic acids research
      title: 'WAR: Webserver for aligning structural RNAs.'
    note: null
    pmcid: PMC2447782
    pmid: '18492721'
    type:
    - Primary
    version: null
  relation: []
  toolType:
  - Web application
  topic:
  - term: Sequence analysis
    uri: http://edamontology.org/topic_0080
  validated: 1
  version:
  - '1'
- accessibility: null
  additionDate: '2019-12-20T15:37:44Z'
  biotoolsCURIE: biotools:IMGT_2Dstructure-DB
  biotoolsID: IMGT_2Dstructure-DB
  collectionID: []
  confidence_flag: null
  cost: Free of charge (with restrictions)
  credit:
  - email: patrice.duroux@igh.cnrs.fr
    fundrefid: null
    gridid: null
    name: Patrice Duroux
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole: []
    url: null
  description: 'IMGT/2Dstructure-DB is the IMGT® database for 2D structures (IMGT
    Colliers de Perles) of immunoglobulins (IG) or antibodies, T cell receptors (TR),
    major histocompatibility (MH) proteins and related proteins of the immune system
    (RPI).

    Annotation is based on the IMGT-ONTOLOGY concepts.'
  documentation:
  - note: null
    type:
    - User manual
    url: http://www.imgt.org/3Dstructure-DB/doc/IMGT3DstructureDBHelp.shtml
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Identifier
        uri: http://edamontology.org/data_0842
      format:
      - term: Textual format
        uri: http://edamontology.org/format_2330
    - data:
        term: Keyword
        uri: http://edamontology.org/data_0968
      format:
      - term: Textual format
        uri: http://edamontology.org/format_2330
    - data:
        term: Ontology concept
        uri: http://edamontology.org/data_2858
      format:
      - term: Textual format
        uri: http://edamontology.org/format_2330
    note: null
    operation:
    - term: Sequence visualisation
      uri: http://edamontology.org/operation_0564
    - term: Query and retrieval
      uri: http://edamontology.org/operation_0224
    - term: Protein secondary structure analysis
      uri: http://edamontology.org/operation_2416
    output:
    - data:
        term: Sequence report
        uri: http://edamontology.org/data_2955
      format:
      - term: HTML
        uri: http://edamontology.org/format_2331
    - data:
        term: Sequence alignment
        uri: http://edamontology.org/data_0863
      format:
      - term: HTML
        uri: http://edamontology.org/format_2331
  homepage: http://www.imgt.org/3Dstructure-DB/
  homepage_status: 0
  language:
  - Perl
  lastUpdate: '2024-11-25T14:00:19.591199Z'
  license: null
  link: []
  maturity: Mature
  name: IMGT 2Dstructure-DB
  operatingSystem:
  - Linux
  - Windows
  - Mac
  otherID: []
  owner: skossida
  publication:
  - doi: 10.1093/nar/gku1056
    metadata:
      abstract: IMGT, the international ImMunoGeneTics information system (http://www.imgt.org)
        is the global reference in immunogenetics and immunoinformatics. By its creation
        in 1989 by Marie-Paule Lefranc (Université de Montpellier and CNRS), IMGT
        marked the advent of immunoinformatics, which emerged at the interface between
        immunogenetics and bioinformatics. IMGT is specialized in the immunoglobulins
        (IG) or antibodies, T cell receptors (TR), major histocompatibility (MH) and
        proteins of the IgSF and MhSF superfamilies. IMGT is built on the IMGTONTOLOGY
        axioms and concepts, which bridged the gap between genes, sequences and 3D
        structures. The concepts include the IMGTR standardized keywords (identification),
        IMGTR standardized labels (description), IMGTR standardized nomenclature (classification),
        IMGT unique numbering and IMGT Colliers de Perles (numerotation). IMGTR comprises
        7 databases, 17 online tools and 15 000 pages of web resources, and provides
        a high-quality and integrated system for analysis of the genomic and expressed
        IG and TR repertoire of the adaptive immune responses, including NGS high-throughput
        data. Tools and databases are used in basic, veterinary and medical research,
        in clinical applications (mutation analysis in leukemia and lymphoma) and
        in antibody engineering and humanization. The IMGT/mAb-DB interface was developed
        for therapeutic antibodies and fusion proteins for immunological applications
        (FPIA). IMGTR is freely available at http://www.imgt.org.
      authors:
      - name: Lefranc M.-P.
      - name: Giudicelli V.
      - name: Duroux P.
      - name: Jabado-Michaloud J.
      - name: Folch G.
      - name: Aouinti S.
      - name: Carillon E.
      - name: Duvergey H.
      - name: Houles A.
      - name: Paysan-Lafosse T.
      - name: Hadi-Saljoqi S.
      - name: Sasorith S.
      - name: Lefranc G.
      - name: Kossida S.
      citationCount: 402
      date: '2015-01-28T00:00:00Z'
      journal: Nucleic Acids Research
      title: IMGT R, the international ImMunoGeneTics information system R 25 years
        on
    note: null
    pmcid: PMC4383898
    pmid: '25378316'
    type: []
    version: null
  relation:
  - biotoolsID: imgt
    type: includedIn
  toolType:
  - Database portal
  topic:
  - term: Immunogenetics
    uri: http://edamontology.org/topic_3930
  - term: Immunoinformatics
    uri: http://edamontology.org/topic_3948
  validated: 0
  version: []
next: ?page=2
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