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  relation: []
  toolType:
  - Web application
  topic:
  - term: Proteins
    uri: http://edamontology.org/topic_0078
  - term: Protein sites, features and motifs
    uri: http://edamontology.org/topic_3510
  - term: Sequence composition, complexity and repeats
    uri: http://edamontology.org/topic_0157
  - term: Gene and protein families
    uri: http://edamontology.org/topic_0623
  - term: Structure prediction
    uri: http://edamontology.org/topic_0082
  validated: 1
  version: []
- accessibility: null
  additionDate: '2025-09-25T05:51:27.623529Z'
  biotoolsCURIE: biotools:masspec
  biotoolsID: masspec
  collectionID: []
  confidence_flag: tool
  cost: null
  credit: []
  description: MASSPEC is (or was) a computer program for the complete sequence analysis
    of large proteins from a single mass spectrum, a precursor to modern-day software
    for de novo sequencing and top-down proteomics.
  documentation: []
  download: []
  editPermission:
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  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Mass spectrum
        uri: http://edamontology.org/data_0943
      format:
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        uri: http://edamontology.org/format_2330
    note: null
    operation:
    - term: Protein sequence analysis
      uri: http://edamontology.org/operation_2479
    output:
    - data:
        term: Protein sequence
        uri: http://edamontology.org/data_2976
      format:
      - term: Textual format
        uri: http://edamontology.org/format_2330
  homepage: https://doi.org/10.1016/0010-4825(70)90013-2
  homepage_status: 0
  language:
  - Fortran
  lastUpdate: '2025-09-25T05:51:27.625976Z'
  license: null
  link: []
  maturity: Legacy
  name: MASSPEC
  operatingSystem: []
  otherID: []
  owner: n.m.palmblad@lumc.nl
  publication:
  - doi: 10.1016/0010-4825(70)90013-2
    metadata:
      abstract: ''
      authors: []
      citationCount: 6
      date: '1970-01-01T00:00:00Z'
      journal: Computers in Biology and Medicine
      title: 'MASSPEC: A computer program for complete sequence analysis of large
        proteins from mass spectrometry data of a single sample'
    note: null
    pmcid: null
    pmid: '5524587'
    type:
    - Primary
    version: null
  relation: []
  toolType:
  - Command-line tool
  topic:
  - term: Proteomics
    uri: http://edamontology.org/topic_0121
  validated: 0
  version: []
- accessibility: null
  additionDate: '2025-09-25T05:45:10.974833Z'
  biotoolsCURIE: biotools:comprotein
  biotoolsID: comprotein
  collectionID: []
  confidence_flag: tool
  cost: null
  credit: []
  description: Comprotein is (or was) a computer program to aid in primary protein
    structure determination, i.e. protein sequencing.
  documentation: []
  download: []
  editPermission:
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  elixirNode: []
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  function:
  - cmd: null
    input: []
    note: null
    operation:
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      uri: http://edamontology.org/operation_2479
    output: []
  homepage: https://dl.acm.org/doi/10.1145/1461518.1461546
  homepage_status: 0
  language:
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  lastUpdate: '2025-09-25T05:45:10.977074Z'
  license: null
  link: []
  maturity: Legacy
  name: Comprotein
  operatingSystem: []
  otherID: []
  owner: n.m.palmblad@lumc.nl
  publication:
  - doi: 10.1145/1461518.1461546
    metadata:
      abstract: ''
      authors: []
      citationCount: 18
      date: '1962-12-04T00:00:00Z'
      journal: AFIPS Conference Proceedings - 1962 Fall Joint Computer Conference,
        AFIPS 1962
      title: 'Comprotein: A computer program to aid primary protein structure determination'
    note: null
    pmcid: null
    pmid: null
    type:
    - Primary
    version: null
  relation: []
  toolType: []
  topic: []
  validated: 0
  version: []
- accessibility: Open access
  additionDate: '2025-09-10T13:36:20.945616Z'
  biotoolsCURIE: biotools:fastplong
  biotoolsID: fastplong
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: null
    fundrefid: null
    gridid: null
    name: OpenGene
    note: 'OpenGene - Open Source Genomics Toolbox

      Open source tools for NGS data analysis'
    orcidid: null
    rorid: null
    typeEntity: null
    typeRole: []
    url: https://github.com/OpenGene
  description: Ultrafast preprocessing and quality control for long reads (Nanopore,
    PacBio, Cyclone, etc.).
  documentation: []
  download: []
  editPermission:
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  elixirNode: []
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  function:
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    input: []
    note: null
    operation:
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      uri: http://edamontology.org/operation_2403
    output: []
  - cmd: null
    input: []
    note: null
    operation:
    - term: Sequencing quality control
      uri: http://edamontology.org/operation_3218
    output: []
  homepage: https://github.com/OpenGene/fastplong
  homepage_status: 0
  language: []
  lastUpdate: '2025-09-10T14:13:36.859562Z'
  license: MIT
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/OpenGene/fastplong
  - note: null
    type:
    - Issue tracker
    url: https://github.com/OpenGene/fastplong/issues
  maturity: null
  name: fastplong
  operatingSystem: []
  otherID: []
  owner: bart
  publication:
  - doi: 10.1002/imt2.107
    metadata:
      abstract: ''
      authors: []
      citationCount: 716
      date: '2023-05-01T00:00:00Z'
      journal: iMeta
      title: Ultrafast one-pass FASTQ data preprocessing, quality control, and deduplication
        using fastp
    note: "Mentioned as Citation in the git repository. \nPublication describes only\
      \ the (short read) tool fastp."
    pmcid: PMC10989850
    pmid: '38868435'
    type:
    - Method
    version: null
  relation: []
  toolType:
  - Command-line tool
  topic:
  - term: Bioinformatics
    uri: http://edamontology.org/topic_0091
  - term: Sequence analysis
    uri: http://edamontology.org/topic_0080
  validated: 0
  version: []
- accessibility: Open access
  additionDate: '2016-03-24T16:22:28Z'
  biotoolsCURIE: biotools:repet
  biotoolsID: repet
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  - elixir-fr-sdp-2019
  - URGI
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  cost: Free of charge
  credit:
  - email: urgi-repet@versailles.inrae.fr
    fundrefid: null
    gridid: null
    name: URGI
    note: 'This tool has a "Numero de depot APP": FR 001 480007 000 R P 2008 000 31
      235'
    orcidid: null
    rorid: null
    typeEntity: Institute
    typeRole:
    - Developer
    - Contributor
    - Maintainer
    - Provider
    - Support
    - Documentor
    url: http://urgi.versailles.inrae.fr/
  description: "The REPET package integrates bioinformatics pipelines dedicated to\
    \ detect, annotate and analyze transposable elements (TEs) in genomic sequences.\
    \ The main pipelines are (i) TEdenovo, which search for interspersed repeats,\
    \ build consensus sequences and classify them according to TE features, and (ii)\n\
    \ TEannot, which mines a genome with a library of TE sequences, for instance the\
    \ one produced by the TEdenovo pipeline, to provide TE annotations exported into\
    \ GFF3 files."
  documentation:
  - note: see also https://urgi.versailles.inrae.fr/Tools/REPET/README
    type:
    - General
    url: https://urgi.versailles.inrae.fr/Tools/REPET
  - note: null
    type:
    - Installation instructions
    url: https://urgi.versailles.inrae.fr/Tools/REPET/INSTALL
  - note: See also https://urgi.versailles.inra.fr/Tools/REPET/TEannot-tuto
    type:
    - User manual
    url: https://urgi.versailles.inrae.fr/Tools/REPET/TEdenovo-tuto
  - note: null
    type:
    - Training material
    url: https://forgemia.inra.fr/urgi-anagen/wiki-repet/-/wikis/REPET-V3.0-tutorial
  download:
  - note: null
    type: Source code
    url: https://urgi.versailles.inrae.fr/download/repet/REPET_linux-x64-3.0.tar.gz
    version: v3.0
  editPermission:
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    - johann_confais
    - raphael.flores
    - cmichotey
    type: group
  elixirCommunity: []
  elixirNode:
  - France
  elixirPlatform:
  - Tools
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: DNA sequence
        uri: http://edamontology.org/data_3494
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
    note: null
    operation:
    - term: Repeat sequence detection
      uri: http://edamontology.org/operation_0379
    - term: Repeat sequence analysis
      uri: http://edamontology.org/operation_0237
    output:
    - data:
        term: DNA sequence
        uri: http://edamontology.org/data_3494
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
    - data:
        term: Feature table
        uri: http://edamontology.org/data_1270
      format:
      - term: Sequence feature table format (text)
        uri: http://edamontology.org/format_2206
    - data:
        term: Annotation track
        uri: http://edamontology.org/data_3002
      format:
      - term: GFF3-seq
        uri: http://edamontology.org/format_1939
  homepage: https://urgi.versailles.inrae.fr/Tools/REPET
  homepage_status: 0
  language:
  - C++
  - Python
  lastUpdate: '2025-09-09T08:10:41.737859Z'
  license: CECILL-2.0
  link:
  - note: null
    type:
    - Repository
    url: https://urgi.versailles.inrae.fr/download/repet/
  maturity: Legacy
  name: REPET
  operatingSystem:
  - Linux
  - Mac
  otherID: []
  owner: Institut Francais de Bioinform
  publication:
  - doi: 10.1371/journal.pone.0091929
    metadata:
      abstract: ''
      authors: []
      citationCount: 226
      date: '2014-05-02T00:00:00Z'
      journal: PLoS ONE
      title: 'PASTEC: An automatic transposable element classification tool'
    note: null
    pmcid: PMC4008368
    pmid: '24786468'
    type:
    - Primary
    version: null
  - doi: 10.1371/journal.pone.0016526
    metadata:
      abstract: ''
      authors: []
      citationCount: 355
      date: '2011-02-09T00:00:00Z'
      journal: PLoS ONE
      title: Considering transposable element diversification in de novo annotation
        approaches
    note: null
    pmcid: PMC3031573
    pmid: '21304975'
    type:
    - Primary
    version: null
  - doi: 10.1371/journal.pcbi.0010022
    metadata:
      abstract: ''
      authors: []
      citationCount: 279
      date: '2005-01-01T00:00:00Z'
      journal: PLoS Computational Biology
      title: Combined evidence annotation of transposable elements in genome sequences
    note: null
    pmcid: PMC1185648
    pmid: '16110336'
    type:
    - Primary
    version: null
  - doi: 10.1007/s00239-003-0007-2
    metadata:
      abstract: ''
      authors: []
      citationCount: 65
      date: '2003-12-29T00:00:00Z'
      journal: Journal of Molecular Evolution
      title: Detection of New Transposable Element Families in Drosophila melanogaster
        and Anopheles gambiae Genomes
    note: null
    pmcid: null
    pmid: '15008403'
    type:
    - Method
    version: null
  - doi: 10.1109/JPROC.2016.2590833
    metadata:
      abstract: ''
      authors: []
      citationCount: 18
      date: '2017-03-01T00:00:00Z'
      journal: Proceedings of the IEEE
      title: 'De Novo Annotation of Transposable Elements: Tackling the Fat Genome
        Issue'
    note: null
    pmcid: null
    pmid: null
    type:
    - Method
    version: null
  relation: []
  toolType:
  - Command-line tool
  topic:
  - term: Sequence composition, complexity and repeats
    uri: http://edamontology.org/topic_0157
  - term: DNA
    uri: http://edamontology.org/topic_0654
  - term: Nucleic acid structure analysis
    uri: http://edamontology.org/topic_0097
  validated: 1
  version:
  - v3.0
- accessibility: null
  additionDate: '2025-07-30T10:37:08.226825Z'
  biotoolsCURIE: biotools:eukrep
  biotoolsID: eukrep
  collectionID: []
  confidence_flag: null
  cost: null
  credit: []
  description: Classification of Eukaryotic and Prokaryotic sequences from metagenomic
    datasets
  documentation: []
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Nucleic acid sequence analysis
      uri: http://edamontology.org/operation_2478
    output: []
  homepage: https://github.com/patrickwest/EukRep
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2025-07-30T10:37:08.229304Z'
  license: MIT
  link: []
  maturity: null
  name: EukRep
  operatingSystem: []
  otherID: []
  owner: m.bernt
  publication:
  - doi: 10.1101/gr.228429.117
    metadata:
      abstract: Microbial eukaryotes are integral components of natural microbial
        communities, and their inclusion is critical for many ecosystem studies, yet
        the majority of published metagenome analyses ignore eukaryotes. In order
        to include eukaryotes in environmental studies, we propose a method to recover
        eukaryotic genomes from complex metagenomic samples. A key step for genome
        recovery is separation of eukaryotic and prokaryotic fragments. We developed
        a k-mer-based strategy, EukRep, for eukaryotic sequence identification and
        applied it to environmental samples to show that it enables genome recovery,
        genome completeness evaluation, and prediction of metabolic potential. We
        used this approach to test the effect of addition of organic carbon on a geyser-associated
        microbial community and detected a substantial change of the community metabolism,
        with selection against almost all candidate phyla bacteria and archaea and
        for eukaryotes. Near complete genomes were reconstructed for three fungi placed
        within the Eurotiomycetes and an arthropod. While carbon fixation and sulfur
        oxidation were important functions in the geyser community prior to carbon
        addition, the organic carbon-impacted community showed enrichment for secreted
        proteases, secreted lipases, cellulose targeting CAZymes, and methanol oxidation.
        We demonstrate the broader utility of EukRep by reconstructing and evaluating
        relatively high-quality fungal, protist, and rotifer genomes from complex
        environmental samples. This approach opens the way for cultivation-independent
        analyses of whole microbial communities.
      authors:
      - name: West P.T.
      - name: Probst A.J.
      - name: Grigoriev I.V.
      - name: Thomas B.C.
      - name: Banfield J.F.
      citationCount: 143
      date: '2018-04-01T00:00:00Z'
      journal: Genome Research
      title: Genome-reconstruction for eukaryotes from complex natural microbial communities
    note: null
    pmcid: null
    pmid: null
    type: []
    version: null
  relation: []
  toolType:
  - Command-line tool
  topic:
  - term: Metagenomics
    uri: http://edamontology.org/topic_3174
  validated: 0
  version: []
- accessibility: null
  additionDate: '2016-09-30T07:30:11Z'
  biotoolsCURIE: biotools:silvangs
  biotoolsID: silvangs
  collectionID:
  - de.NBI
  - de.NBI-biodata
  - DSMZ Digital Diversity
  confidence_flag: null
  cost: Free of charge (with restrictions)
  credit:
  - email: ngs-contact@arb-silva.de
    fundrefid: null
    gridid: grid.507782.f
    name: SILVA Team
    note: null
    orcidid: null
    rorid: 027z9pz32
    typeEntity: Division
    typeRole:
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    url: https://www.arb-silva.de/contact/team/
  - email: hub@dsmz.de
    fundrefid: null
    gridid: grid.420081.f
    name: Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures
    note: null
    orcidid: null
    rorid: 02tyer376
    typeEntity: Institute
    typeRole:
    - Provider
    url: https://www.dsmz.de
  description: SILVAngs is a data analysis service for ribosomal RNA gene (rDNA) amplicon
    reads from high-throughput sequencing (next-generation sequencing (NGS)) approaches
    based on an automatic software pipeline. It uses the SILVA rDNA databases, taxonomies,
    and alignments as a reference. It facilitates the classification of rDNA reads
    and provides a wealth of results (tables, graphs and sequence files) for download.
  documentation:
  - note: null
    type:
    - User manual
    url: https://www.arb-silva.de/fileadmin/silva_databases/sngs/SILVAngs_User_Guide.pdf
  - note: null
    type:
    - FAQ
    url: https://www.arb-silva.de/documentation/silvangs/userfaq/
  - note: null
    type:
    - Terms of use
    url: https://www.arb-silva.de/footer/sngs-termsofuse
  download: []
  editPermission:
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    type: group
  elixirCommunity: []
  elixirNode:
  - Germany
  elixirPlatform:
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  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Nucleic acid sequence
        uri: http://edamontology.org/data_2977
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
    note: The pipeline accepts input data in Multi-Fasta format with each input file
      representing one sample. Samples that belong to one project (a transect, timeseries
      etc.) should be uploaded as a single SILVAngs project.
    operation:
    - term: Visualisation
      uri: http://edamontology.org/operation_0337
    - term: Statistical calculation
      uri: http://edamontology.org/operation_2238
    - term: Nucleic acid sequence analysis
      uri: http://edamontology.org/operation_2478
    - term: Taxonomic classification
      uri: http://edamontology.org/operation_3460
    - term: Validation
      uri: http://edamontology.org/operation_2428
    - term: Sequence clustering
      uri: http://edamontology.org/operation_0291
    - term: Sequence alignment
      uri: http://edamontology.org/operation_0292
    output:
    - data:
        term: Matrix
        uri: http://edamontology.org/data_2082
      format:
      - term: TSV
        uri: http://edamontology.org/format_3475
    - data:
        term: Plot
        uri: http://edamontology.org/data_2884
      format: []
    - data:
        term: Report
        uri: http://edamontology.org/data_2048
      format:
      - term: PDF
        uri: http://edamontology.org/format_3508
    - data:
        term: Sequence cluster (nucleic acid)
        uri: http://edamontology.org/data_1246
      format:
      - term: FASTA-aln
        uri: http://edamontology.org/format_1984
    - data:
        term: Nucleic acid sequence
        uri: http://edamontology.org/data_2977
      format:
      - term: ARB
        uri: http://edamontology.org/format_3830
      - term: FASTA-aln
        uri: http://edamontology.org/format_1984
  homepage: https://ngs.arb-silva.de
  homepage_status: 0
  language: []
  lastUpdate: '2025-06-30T13:26:39.251875Z'
  license: null
  link: []
  maturity: Mature
  name: SILVAngs
  operatingSystem: []
  otherID: []
  owner: silva
  publication:
  - doi: 10.1093/nar/gks1219
    metadata:
      abstract: SILVA (from Latin silva, forest, http://www.arb-silva.de) is a comprehensive
        web resource for up to date, quality-controlled databases of aligned ribosomal
        RNA (rRNA) gene sequences from the Bacteria, Archaea and Eukaryota domains
        and supplementary online services. The referred database release 111 (July
        2012) contains 3194 778 small subunit and 288717 large subunit rRNA gene sequences.
        Since the initial description of the project, substantial new features have
        been introduced, including advanced quality control procedures, an improved
        rRNA gene aligner, online tools for probe and primer evaluation and optimized
        browsing, searching and downloading on the website. Furthermore, the extensively
        curated SILVA taxonomy and the new non-redundant SILVA datasets provide an
        ideal reference for high-throughput classification of data from next-generation
        sequencing approaches. © The Author(s) 2012.
      authors:
      - name: Quast C.
      - name: Pruesse E.
      - name: Yilmaz P.
      - name: Gerken J.
      - name: Schweer T.
      - name: Yarza P.
      - name: Peplies J.
      - name: Glockner F.O.
      citationCount: 22633
      date: '2013-01-01T00:00:00Z'
      journal: Nucleic Acids Research
      title: 'The SILVA ribosomal RNA gene database project: Improved data processing
        and web-based tools'
    note: null
    pmcid: PMC3531112
    pmid: '23193283'
    type:
    - Primary
    version: null
  - doi: 10.1093/nar/gkt1209
    metadata:
      abstract: SILVA (from Latin silva, forest, http://www.arb-silva.de) is a comprehensive
        resource for up-to-date quality-controlled databases of aligned ribosomal
        RNA (rRNA) gene sequences from the Bacteria, Archaea and Eukaryota domains
        and supplementary online services. SILVA provides a manually curated taxonomy
        for all three domains of life, based on representative phylogenetic trees
        for the small- and large-subunit rRNA genes. This article describes the improvements
        the SILVA taxonomy has undergone in the last 3 years. Specifically we are
        focusing on the curation process, the various resources used for curation
        and the comparison of the SILVA taxonomy with Greengenes and RDP-II taxonomies.
        Our comparisons not only revealed a reasonable overlap between the taxa names,
        but also points to significant differences in both names and numbers of taxa
        between the three resources. © 2013 The Author(s). Published by Oxford University
        Press.
      authors:
      - name: Yilmaz P.
      - name: Parfrey L.W.
      - name: Yarza P.
      - name: Gerken J.
      - name: Pruesse E.
      - name: Quast C.
      - name: Schweer T.
      - name: Peplies J.
      - name: Ludwig W.
      - name: Glockner F.O.
      citationCount: 2590
      date: '2014-01-01T00:00:00Z'
      journal: Nucleic Acids Research
      title: The SILVA and "all-species Living Tree Project (LTP)" taxonomic frameworks
    note: null
    pmcid: PMC3965112
    pmid: '24293649'
    type:
    - Primary
    version: null
  - doi: 10.1093/bioinformatics/bts252
    metadata:
      abstract: 'Motivation: In the analysis of homologous sequences, computation
        of multiple sequence alignments (MSAs) has become a bottleneck. This is especially
        troublesome for marker genes like the ribosomal RNA (rRNA) where already millions
        of sequences are publicly available and individual studies can easily produce
        hundreds of thousands of new sequences. Methods have been developed to cope
        with such numbers, but further improvements are needed to meet accuracy requirements.Results:
        In this study, we present the SILVA Incremental Aligner (SINA) used to align
        the rRNA gene databases provided by the SILVA ribosomal RNA project. SINA
        uses a combination of k-mer searching and partial order alignment (POA) to
        maintain very high alignment accuracy while satisfying high throughput performance
        demands. SINA was evaluated in comparison with the commonly used high throughput
        MSA programs PyNAST and mothur. The three BRAliBase III benchmark MSAs could
        be reproduced with 99.3, 97.6 and 96.1 accuracy. A larger benchmark MSA comprising
        38 772 sequences could be reproduced with 98.9 and 99.3% accuracy using reference
        MSAs comprising 1000 and 5000 sequences. SINA was able to achieve higher accuracy
        than PyNAST and mothur in all performed benchmarks. © The Author(s) 2012.
        Published by Oxford University Press.'
      authors:
      - name: Pruesse E.
      - name: Peplies J.
      - name: Glockner F.O.
      citationCount: 2408
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    note: null
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    type:
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    version: null
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  - term: Biodiversity
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  - term: Functional, regulatory and non-coding RNA
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  - term: Sequence analysis
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  - term: Microbial ecology
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- accessibility: null
  additionDate: '2018-07-01T13:17:42Z'
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    note: null
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    rorid: null
    typeEntity: Person
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  - note: null
    type:
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  license: null
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  maturity: null
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      journal: Bioinformatics
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  - Python
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  description: neXtProt was an innovative knowledge platform dedicated to human proteins.
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