count: 919
list:
- accessibility: null
  additionDate: '2016-01-19T16:39:56Z'
  biotoolsCURIE: biotools:openms
  biotoolsID: openms
  collectionID:
  - KNIME
  - de.NBI
  - Proteomics
  - OpenMS
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: null
    fundrefid: null
    gridid: null
    name: ETH Zürich
    note: null
    orcidid: null
    rorid: null
    typeEntity: Institute
    typeRole:
    - Provider
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Eberhard-Karls-Universität Tübingen
    note: null
    orcidid: null
    rorid: null
    typeEntity: Institute
    typeRole:
    - Provider
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Freie Universität Berlin
    note: null
    orcidid: null
    rorid: null
    typeEntity: Institute
    typeRole:
    - Provider
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Center for Integrative Bioinformatics (CiBi)
    note: null
    orcidid: null
    rorid: null
    typeEntity: Consortium
    typeRole: []
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: cibi
    note: null
    orcidid: null
    rorid: null
    typeEntity: Institute
    typeRole:
    - Provider
    url: null
  - email: open-ms-general@lists.sourceforge.net
    fundrefid: null
    gridid: null
    name: General Mailinglist
    note: null
    orcidid: null
    rorid: null
    typeEntity: null
    typeRole:
    - Support
    url: null
  - email: open-ms-general@lists.sourceforge.net
    fundrefid: null
    gridid: null
    name: General Mailinglist
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Hannes Röst
    note: null
    orcidid: http://orcid.org/0000-0003-0990-7488
    rorid: null
    typeEntity: Person
    typeRole:
    - Contributor
    url: null
  description: Open source library and a collection of tools and interfaces for the
    analysis of mass spectrometry data. Includes over 200 standalone (TOPP) tools
    that can be combined to a workflow with the integrated workflow editor TOPPAS.
    Raw and intermediate mass spectrometry data can be visualised with the included
    viewer TOPPView.
  documentation:
  - note: null
    type:
    - General
    url: http://ftp.mi.fu-berlin.de/pub/OpenMS/release-documentation/html/index.html
  download:
  - note: null
    type: Source code
    url: https://github.com/OpenMS/OpenMS
    version: null
  - note: null
    type: Binaries
    url: http://sourceforge.net/projects/open-ms/files/OpenMS/OpenMS-2.0/
    version: null
  - note: null
    type: Source code
    url: https://github.com/OpenMS/OpenMS
    version: null
  editPermission:
    authors:
    - proteomics.bio.tools
    type: group
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Mass spectrometry data
        uri: http://edamontology.org/data_2536
      format:
      - term: pepXML
        uri: http://edamontology.org/format_3655
      - term: mzQuantML
        uri: http://edamontology.org/format_3248
      - term: dta
        uri: http://edamontology.org/format_3652
      - term: FASTA
        uri: http://edamontology.org/format_1929
      - term: protXML
        uri: http://edamontology.org/format_3747
      - term: idXML
        uri: http://edamontology.org/format_3764
      - term: OBO
        uri: http://edamontology.org/format_2549
      - term: XML
        uri: http://edamontology.org/format_2332
      - term: TraML
        uri: http://edamontology.org/format_3246
      - term: mzML
        uri: http://edamontology.org/format_3244
      - term: mzIdentML
        uri: http://edamontology.org/format_3247
      - term: mzXML
        uri: http://edamontology.org/format_3654
      - term: MGF
        uri: http://edamontology.org/format_3651
      - term: qcML
        uri: http://edamontology.org/format_3683
    - data:
        term: Sequence record
        uri: http://edamontology.org/data_0849
      format:
      - term: pepXML
        uri: http://edamontology.org/format_3655
      - term: mzQuantML
        uri: http://edamontology.org/format_3248
      - term: dta
        uri: http://edamontology.org/format_3652
      - term: FASTA
        uri: http://edamontology.org/format_1929
      - term: protXML
        uri: http://edamontology.org/format_3747
      - term: idXML
        uri: http://edamontology.org/format_3764
      - term: OBO
        uri: http://edamontology.org/format_2549
      - term: XML
        uri: http://edamontology.org/format_2332
      - term: TraML
        uri: http://edamontology.org/format_3246
      - term: mzML
        uri: http://edamontology.org/format_3244
      - term: mzIdentML
        uri: http://edamontology.org/format_3247
      - term: mzXML
        uri: http://edamontology.org/format_3654
      - term: MGF
        uri: http://edamontology.org/format_3651
      - term: qcML
        uri: http://edamontology.org/format_3683
    - data:
        term: Peptide identification
        uri: http://edamontology.org/data_0945
      format:
      - term: pepXML
        uri: http://edamontology.org/format_3655
      - term: mzQuantML
        uri: http://edamontology.org/format_3248
      - term: dta
        uri: http://edamontology.org/format_3652
      - term: FASTA
        uri: http://edamontology.org/format_1929
      - term: protXML
        uri: http://edamontology.org/format_3747
      - term: idXML
        uri: http://edamontology.org/format_3764
      - term: OBO
        uri: http://edamontology.org/format_2549
      - term: XML
        uri: http://edamontology.org/format_2332
      - term: TraML
        uri: http://edamontology.org/format_3246
      - term: mzML
        uri: http://edamontology.org/format_3244
      - term: mzIdentML
        uri: http://edamontology.org/format_3247
      - term: mzXML
        uri: http://edamontology.org/format_3654
      - term: MGF
        uri: http://edamontology.org/format_3651
      - term: qcML
        uri: http://edamontology.org/format_3683
    note: null
    operation:
    - term: Protein identification
      uri: http://edamontology.org/operation_3767
    - term: Parsing
      uri: http://edamontology.org/operation_1812
    - term: Data handling
      uri: http://edamontology.org/operation_2409
    - term: Chromatographic alignment
      uri: http://edamontology.org/operation_3628
    - term: Mass spectra calibration
      uri: http://edamontology.org/operation_3627
    - term: Formatting
      uri: http://edamontology.org/operation_0335
    - term: Protein quantification
      uri: http://edamontology.org/operation_3630
    - term: Retention time prediction
      uri: http://edamontology.org/operation_3633
    - term: Annotation
      uri: http://edamontology.org/operation_0226
    - term: Protein feature detection
      uri: http://edamontology.org/operation_3092
    - term: Isotope-coded protein label
      uri: http://edamontology.org/operation_3705
    - term: Label-free quantification
      uri: http://edamontology.org/operation_3634
    - term: iTRAQ
      uri: http://edamontology.org/operation_3639
    - term: Peptide identification
      uri: http://edamontology.org/operation_3631
    - term: Peak detection
      uri: http://edamontology.org/operation_3215
    - term: Mass spectrum visualisation
      uri: http://edamontology.org/operation_3694
    - term: Labeled quantification
      uri: http://edamontology.org/operation_3635
    - term: Splitting
      uri: http://edamontology.org/operation_3359
    - term: Spectral analysis
      uri: http://edamontology.org/operation_3214
    - term: Deisotoping
      uri: http://edamontology.org/operation_3629
    - term: Target-Decoy
      uri: http://edamontology.org/operation_3649
    - term: Prediction and recognition (protein)
      uri: http://edamontology.org/operation_3023
    - term: Comparison
      uri: http://edamontology.org/operation_2424
    - term: Standardisation and normalisation
      uri: http://edamontology.org/operation_3435
    output:
    - data:
        term: Peptide identification
        uri: http://edamontology.org/data_0945
      format:
      - term: pepXML
        uri: http://edamontology.org/format_3655
      - term: mzQuantML
        uri: http://edamontology.org/format_3248
      - term: dta
        uri: http://edamontology.org/format_3652
      - term: FASTA
        uri: http://edamontology.org/format_1929
      - term: idXML
        uri: http://edamontology.org/format_3764
      - term: mzXML
        uri: http://edamontology.org/format_3654
      - term: TraML
        uri: http://edamontology.org/format_3246
      - term: mzML
        uri: http://edamontology.org/format_3244
      - term: mzIdentML
        uri: http://edamontology.org/format_3247
      - term: MGF
        uri: http://edamontology.org/format_3651
      - term: qcML
        uri: http://edamontology.org/format_3683
    - data:
        term: Expression data
        uri: http://edamontology.org/data_2603
      format:
      - term: pepXML
        uri: http://edamontology.org/format_3655
      - term: mzQuantML
        uri: http://edamontology.org/format_3248
      - term: dta
        uri: http://edamontology.org/format_3652
      - term: FASTA
        uri: http://edamontology.org/format_1929
      - term: idXML
        uri: http://edamontology.org/format_3764
      - term: mzXML
        uri: http://edamontology.org/format_3654
      - term: TraML
        uri: http://edamontology.org/format_3246
      - term: mzML
        uri: http://edamontology.org/format_3244
      - term: mzIdentML
        uri: http://edamontology.org/format_3247
      - term: MGF
        uri: http://edamontology.org/format_3651
      - term: qcML
        uri: http://edamontology.org/format_3683
  homepage: http://www.openms.de
  homepage_status: 0
  language:
  - C++
  lastUpdate: '2025-04-30T11:39:30.251890Z'
  license: BSD-3-Clause
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/OpenMS/OpenMS
  maturity: Mature
  name: OpenMS
  operatingSystem:
  - Linux
  - Windows
  - Mac
  otherID: []
  owner: samwein
  publication:
  - doi: 10.1038/nmeth.3959
    metadata:
      abstract: © 2016 Nature America, Inc. All rights reserved.High-resolution mass
        spectrometry (MS) has become an important tool in the life sciences, contributing
        to the diagnosis and understanding of human diseases, elucidating biomolecular
        structural information and characterizing cellular signaling networks. However,
        the rapid growth in the volume and complexity of MS data makes transparent,
        accurate and reproducible analysis difficult. We present OpenMS 2.0 (http://www.openms.de),
        a robust, open-source, cross-platform software specifically designed for the
        flexible and reproducible analysis of high-throughput MS data. The extensible
        OpenMS software implements common mass spectrometric data processing tasks
        through a well-defined application programming interface in C++ and Python
        and through standardized open data formats. OpenMS additionally provides a
        set of 185 tools and ready-made workflows for common mass spectrometric data
        processing tasks, which enable users to perform complex quantitative mass
        spectrometric analyses with ease.
      authors:
      - name: Rost H.L.
      - name: Sachsenberg T.
      - name: Aiche S.
      - name: Bielow C.
      - name: Weisser H.
      - name: Aicheler F.
      - name: Andreotti S.
      - name: Ehrlich H.-C.
      - name: Gutenbrunner P.
      - name: Kenar E.
      - name: Liang X.
      - name: Nahnsen S.
      - name: Nilse L.
      - name: Pfeuffer J.
      - name: Rosenberger G.
      - name: Rurik M.
      - name: Schmitt U.
      - name: Veit J.
      - name: Walzer M.
      - name: Wojnar D.
      - name: Wolski W.E.
      - name: Schilling O.
      - name: Choudhary J.S.
      - name: Malmstrom L.
      - name: Aebersold R.
      - name: Reinert K.
      - name: Kohlbacher O.
      citationCount: 246
      date: '2016-08-30T00:00:00Z'
      journal: Nature Methods
      title: 'OpenMS: A flexible open-source software platform for mass spectrometry
        data analysis'
    note: null
    pmcid: null
    pmid: '27575624'
    type:
    - Primary
    version: null
  - doi: 10.1007/978-1-60761-987-1_23
    metadata:
      abstract: Proteomics experiments based on state-of-the-art mass spectrometry
        produce vast amounts of data, which cannot be analyzed manually. Hence, software
        is needed which is able to analyze the data in an automated fashion. The need
        for robust and reusable software tools triggered the development of libraries
        implementing different algorithms for the various analysis steps. OpenMS is
        such a software library and provides a wealth of data structures and algorithms
        for the analysis of mass spectrometric data. For users unfamiliar with programming,
        TOPP ("The OpenMS Proteomics Pipeline") offers a wide range of already implemented
        tools sharing the same interface and designed for a specific analysis task
        each. TOPP thus makes the sophisticated algorithms of OpenMS accessible to
        nonprogrammers. The individual TOPP tools can be strung together into pipelines
        for analyzing mass spectrometry-based experiments starting from the raw output
        of the mass spectrometer. These analysis pipelines can be constructed using
        a graphical editor. Even complex analytical workflows can thus be analyzed
        with ease.
      authors:
      - name: Bertsch A.
      - name: Gropl C.
      - name: Reinert K.
      - name: Kohlbacher O.
      citationCount: 65
      date: '2011-01-01T00:00:00Z'
      journal: Methods in molecular biology (Clifton, N.J.)
      title: 'OpenMS and TOPP: open source software for LC-MS data analysis.'
    note: null
    pmcid: null
    pmid: null
    type:
    - Other
    version: null
  relation: []
  toolType:
  - Library
  - Workbench
  topic:
  - term: Proteomics experiment
    uri: http://edamontology.org/topic_3520
  - term: Proteomics
    uri: http://edamontology.org/topic_0121
  - term: Metabolomics
    uri: http://edamontology.org/topic_3172
  validated: 1
  version:
  - 2.0.0
- accessibility: null
  additionDate: '2017-08-20T15:57:59Z'
  biotoolsCURIE: biotools:metaphlan
  biotoolsID: metaphlan
  collectionID:
  - Animal and Crop Genomics
  confidence_flag: null
  cost: null
  credit:
  - email: null
    fundrefid: null
    gridid: null
    name: null
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: https://groups.google.com/forum/#!forum/metaphlan-users
  description: Computational tool for profiling the composition of microbial communities
    from metagenomic shotgun sequencing data.
  documentation:
  - note: null
    type:
    - General
    url: https://github.com/biobakery/MetaPhlAn
  download: []
  editPermission:
    authors:
    - animalandcropgenomics
    - ELIXIR-CZ
    - bebatut
    - vashokan
    type: group
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: metaphlan <fastq_input> --input_type fastq -o <output>
    input:
    - data:
        term: DNA sequence
        uri: http://edamontology.org/data_3494
      format:
      - term: FASTQ
        uri: http://edamontology.org/format_1930
      - term: FASTA
        uri: http://edamontology.org/format_1929
      - term: SAM
        uri: http://edamontology.org/format_2573
    note: null
    operation:
    - term: Taxonomic classification
      uri: http://edamontology.org/operation_3460
    output:
    - data:
        term: Taxonomy
        uri: http://edamontology.org/data_3028
      format:
      - term: DSV
        uri: http://edamontology.org/format_3751
  - cmd: sgb_to_gtdb_profile.py -i <metaphlan_output> -o <gtdb_metaphlan_output>
    input:
    - data:
        term: Taxonomy
        uri: http://edamontology.org/data_3028
      format:
      - term: DSV
        uri: http://edamontology.org/format_3751
    note: Convert SGB-based profile to GTDB taxonomy
    operation:
    - term: Taxonomic classification
      uri: http://edamontology.org/operation_3460
    output:
    - data:
        term: Taxonomy
        uri: http://edamontology.org/data_3028
      format:
      - term: DSV
        uri: http://edamontology.org/format_3751
  homepage: http://segatalab.cibio.unitn.it/tools/metaphlan/index.html
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2025-04-22T12:44:24.859435Z'
  license: MIT
  link: []
  maturity: null
  name: MetaPhlAn
  operatingSystem:
  - Linux
  - Windows
  - Mac
  otherID: []
  owner: admin
  publication:
  - doi: 10.1038/nmeth.2066
    metadata:
      abstract: Metagenomic shotgun sequencing data can identify microbes populating
        a microbial community and their proportions, but existing taxonomic profiling
        methods are inefficient for increasingly large data sets. We present an approach
        that uses clade-specific marker genes to unambiguously assign reads to microbial
        clades more accurately and >50Ã-faster than current approaches. We validated
        our metagenomic phylogenetic analysis tool, MetaPhlAn, on terabases of short
        reads and provide the largest metagenomic profiling to date of the human gut.
        It can be accessed at http://huttenhower.sph.harvard.edu/ metaphlan/. © 2012
        Nature America, Inc. All rights reserved.
      authors:
      - name: Segata N.
      - name: Waldron L.
      - name: Ballarini A.
      - name: Narasimhan V.
      - name: Jousson O.
      - name: Huttenhower C.
      citationCount: 1300
      date: '2012-08-01T00:00:00Z'
      journal: Nature Methods
      title: Metagenomic microbial community profiling using unique clade-specific
        marker genes
    note: null
    pmcid: PMC3443552
    pmid: '22688413'
    type:
    - Primary
    version: null
  relation: []
  toolType:
  - Command-line tool
  topic:
  - term: Metagenomics
    uri: http://edamontology.org/topic_3174
  - term: Phylogenomics
    uri: http://edamontology.org/topic_0194
  validated: 1
  version: []
- accessibility: null
  additionDate: '2015-06-29T10:14:28Z'
  biotoolsCURIE: biotools:netpicorna
  biotoolsID: netpicorna
  collectionID: []
  confidence_flag: null
  cost: Free of charge (with restrictions)
  credit:
  - email: null
    fundrefid: null
    gridid: null
    name: CBS
    note: null
    orcidid: null
    rorid: null
    typeEntity: Institute
    typeRole:
    - Provider
    url: null
  - email: nikob@cbs.dtu.dk
    fundrefid: null
    gridid: null
    name: Nikolaj Sorgenfrei Blom
    note: null
    orcidid: https://orcid.org/0000-0001-7787-7853
    rorid: null
    typeEntity: Person
    typeRole: []
    url: null
  description: Neural network predictions of cleavage sites of picornaviral proteases.
  documentation:
  - note: null
    type:
    - General
    url: http://www.cbs.dtu.dk/services/NetPicoRNA/instructions.php
  download: []
  editPermission:
    authors:
    - powehi
    type: group
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Sequence
        uri: http://edamontology.org/data_2044
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
    note: produces neural network predictions of cleavage sites of picornaviral proteases
    operation:
    - term: Protein cleavage site prediction
      uri: http://edamontology.org/operation_0422
    output:
    - data:
        term: Protein features
        uri: http://edamontology.org/data_1277
      format:
      - term: Textual format
        uri: http://edamontology.org/format_2330
    - data:
        term: Sequence report
        uri: http://edamontology.org/data_2955
      format:
      - term: Binary format
        uri: http://edamontology.org/format_2333
  homepage: http://cbs.dtu.dk/services/NetPicoRNA/
  homepage_status: 0
  language: []
  lastUpdate: '2025-04-21T12:49:56.070719Z'
  license: Other
  link:
  - note: null
    type:
    - Software catalogue
    url: http://cbs.dtu.dk/services
  maturity: Legacy
  name: NetPicoRNA
  operatingSystem:
  - Linux
  otherID: []
  owner: powehi
  publication:
  - doi: 10.1002/pro.5560051107
    metadata:
      abstract: Picornaviral proteinases are responsible for maturation cleavages
        of the viral polyprotein, but also catalyze the degradation of cellular targets.
        Using graphical visualization techniques and neural network algorithms, we
        have investigated the sequence specificity of the two proteinases 2A(pro)
        and 3C(pro). The cleavage of VP0 (giving rise to VP2 and VP4), which is carried
        out by a so-far unknown proteinase, was also examined. In combination with
        a novel surface exposure prediction algorithm, our neural network approach
        successfully distinguishes known cleavage sites from noncleavage sites and
        yields a more consistent definition of features common to these sites. The
        method is able to predict experimentally determined cleavage sites in cellular
        proteins. We present a list of mammalian and other proteins that are predicted
        to be possible targets for the vital proteinases. Whether these proteins are
        indeed cleaved awaits experimental verification. Additionally, we report several
        errors detected in the protein databases.
      authors:
      - name: Blom N.
      - name: Hansen J.
      - name: Blaas D.
      - name: Brunak S.
      citationCount: 204
      date: '1996-01-01T00:00:00Z'
      journal: Protein Science
      title: 'Cleavage site analysis in picornaviral polyproteins: Discovering cellular
        targets by neural networks'
    note: null
    pmcid: PMC2143287
    pmid: '8931139'
    type:
    - Primary
    version: null
  relation: []
  toolType:
  - Web application
  topic:
  - term: Protein sites, features and motifs
    uri: http://edamontology.org/topic_3510
  - term: Sequence sites, features and motifs
    uri: http://edamontology.org/topic_0160
  validated: 1
  version:
  - '1.0'
- accessibility: Open access
  additionDate: '2025-02-28T15:04:33.594183Z'
  biotoolsCURIE: biotools:prolfquapp
  biotoolsID: prolfquapp
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit: []
  description: A command-line tool for differential expression analysis in quantitative
    proteomics
  documentation:
  - note: null
    type:
    - General
    url: https://github.com/prolfqua/prolfquapp/blob/master/README.md
  download:
  - note: null
    type: Downloads page
    url: https://github.com/prolfqua/prolfquapp/releases/tag/0.1.6
    version: 0.1.6
  editPermission:
    authors:
    - thatmariia
    type: group
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: './prolfqua_dea.sh -i data_dir/ -d annotation.xlsx -y config.yaml -w NameOfAnalysis
      -s DIANN

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

      # ./prolfquapp_docker.sh prolfqua_dea.sh -i data_dir/ -d annotation.xlsx -y
      config.yaml -w NameOfAnalysis -s DIANN'
    input:
    - data:
        term: Expression data
        uri: http://edamontology.org/data_2603
      format:
      - term: CSV
        uri: http://edamontology.org/format_3752
      - term: TSV
        uri: http://edamontology.org/format_3475
    - data:
        term: Sequence
        uri: http://edamontology.org/data_2044
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
    note: null
    operation:
    - term: Differential protein expression profiling
      uri: http://edamontology.org/operation_3741
    output:
    - data:
        term: Expression data
        uri: http://edamontology.org/data_2603
      format:
      - term: xlsx
        uri: http://edamontology.org/format_3620
      - term: HTML
        uri: http://edamontology.org/format_2331
  - cmd: null
    input:
    - data:
        term: Expression data
        uri: http://edamontology.org/data_2603
      format:
      - term: xlsx
        uri: http://edamontology.org/format_3620
    note: null
    operation:
    - term: Validation
      uri: http://edamontology.org/operation_2428
    output:
    - data:
        term: Quality control report
        uri: http://edamontology.org/data_3914
      format:
      - term: HTML
        uri: http://edamontology.org/format_2331
  - cmd: null
    input:
    - data:
        term: Expression data
        uri: http://edamontology.org/data_2603
      format:
      - term: CSV
        uri: http://edamontology.org/format_3752
      - term: TSV
        uri: http://edamontology.org/format_3475
    - data:
        term: Protein sequence
        uri: http://edamontology.org/data_2976
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
    note: null
    operation:
    - term: Expression data visualisation
      uri: http://edamontology.org/operation_0571
    output:
    - data:
        term: Expression data
        uri: http://edamontology.org/data_2603
      format:
      - term: PDF
        uri: http://edamontology.org/format_3508
      - term: HTML
        uri: http://edamontology.org/format_2331
  homepage: https://github.com/prolfqua/prolfquapp
  homepage_status: 0
  language:
  - R
  lastUpdate: '2025-03-28T10:18:25.715685Z'
  license: MIT
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/prolfqua/prolfquapp
  - note: null
    type:
    - Issue tracker
    url: https://github.com/prolfqua/prolfquapp/issues
  maturity: Emerging
  name: prolfquapp
  operatingSystem:
  - Mac
  - Linux
  otherID: []
  owner: n.m.palmblad@lumc.nl
  publication:
  - doi: 10.1021/acs.jproteome.4c00911
    metadata:
      abstract: Mass spectrometry is a cornerstone of quantitative proteomics, enabling
        relative protein quantification and differential expression analysis (DEA)
        of proteins. As experiments grow in complexity, involving more samples, groups,
        and identified proteins, interactive differential expression analysis tools
        become impractical. The prolfquapp addresses this challenge by providing a
        command-line interface that simplifies DEA, making it accessible to nonprogrammers
        and seamlessly integrating it into workflow management systems. Prolfquapp
        streamlines data processing and result visualization by generating dynamic
        HTML reports that facilitate the exploration of differential expression results.
        These reports allow for investigating complex experiments, such as those involving
        repeated measurements or multiple explanatory variables. Additionally, prolfquapp
        supports various output formats, including XLSX files, SummarizedExperiment
        objects and rank files, for further interactive analysis using spreadsheet
        software, the exploreDE Shiny application, or gene set enrichment analysis
        software, respectively. By leveraging advanced statistical models from the
        prolfqua R package, prolfquapp offers a user-friendly, integrated solution
        for large-scale quantitative proteomics studies, combining efficient data
        processing with insightful, publication-ready outputs.
      authors:
      - name: Wolski W.E.
      - name: Grossmann J.
      - name: Schwarz L.
      - name: Leary P.
      - name: Turker C.
      - name: Nanni P.
      - name: Schlapbach R.
      - name: Panse C.
      citationCount: 0
      date: '2025-02-07T00:00:00Z'
      journal: Journal of Proteome Research
      title: prolfquapp ─ A User-Friendly Command-Line Tool Simplifying Differential
        Expression Analysis in Quantitative Proteomics
    note: null
    pmcid: null
    pmid: null
    type: []
    version: 0.0.6
  relation: []
  toolType:
  - Command-line tool
  topic:
  - term: Proteomics
    uri: http://edamontology.org/topic_0121
  validated: 0
  version:
  - 0.1.6
- accessibility: Open access
  additionDate: '2025-01-31T17:19:47.094256Z'
  biotoolsCURIE: biotools:proteomaker
  biotoolsID: proteomaker
  collectionID:
  - Proteomics
  confidence_flag: null
  cost: Free of charge
  credit: []
  description: ProteoMaker is a platform for the generation of an in-silico bottom-up
    proteomics data set with a ground truth on the level of proteoforms.
  documentation: []
  download:
  - note: null
    type: Source code
    url: https://github.com/computproteomics/ProteoMaker
    version: null
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Protein sequence
        uri: http://edamontology.org/data_2976
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
    note: null
    operation:
    - term: Simulated gene expression data generation
      uri: http://edamontology.org/operation_3566
    - term: Statistical calculation
      uri: http://edamontology.org/operation_2238
    output:
    - data:
        term: Gene expression matrix
        uri: http://edamontology.org/data_3112
      format:
      - term: CSV
        uri: http://edamontology.org/format_3752
    - data:
        term: Proteolytic digest
        uri: http://edamontology.org/data_1238
      format:
      - term: CSV
        uri: http://edamontology.org/format_3752
    - data:
        term: Quality control report
        uri: http://edamontology.org/data_3914
      format:
      - term: YAML
        uri: http://edamontology.org/format_3750
    - data:
        term: Statistical estimate score
        uri: http://edamontology.org/data_0951
      format:
      - term: CSV
        uri: http://edamontology.org/format_3752
  homepage: https://github.com/computproteomics/ProteoMaker
  homepage_status: 0
  language:
  - R
  lastUpdate: '2025-01-31T17:19:47.096981Z'
  license: MIT
  link:
  - note: Web application
    type:
    - Service
    url: https://computproteomics.bmb.sdu.dk/app_direct/ProteoMaker
  maturity: Mature
  name: ProteoMaker
  operatingSystem:
  - Mac
  - Linux
  - Windows
  otherID: []
  owner: veitveit11
  publication: []
  relation: []
  toolType:
  - Library
  - Web application
  topic:
  - term: Proteomics
    uri: http://edamontology.org/topic_0121
  - term: Proteomics experiment
    uri: http://edamontology.org/topic_3520
  - term: Simulation experiment
    uri: http://edamontology.org/topic_3524
  validated: 0
  version: []
- accessibility: Open access
  additionDate: '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: null
    name: null
    note: null
    orcidid: null
    rorid: null
    typeEntity: Project
    typeRole:
    - Primary contact
    url: null
  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: http://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
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode:
  - Germany
  elixirPlatform:
  - Data
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Sequence accession (nucleic acid)
        uri: http://edamontology.org/data_1097
      format:
      - term: plain text format (unformatted)
        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
        uri: http://edamontology.org/data_1046
      format:
      - term: plain text format (unformatted)
        uri: http://edamontology.org/format_1964
    - data:
        term: Article ID
        uri: http://edamontology.org/data_1088
      format:
      - term: plain text format (unformatted)
        uri: http://edamontology.org/format_1964
    - data:
        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:
    - data:
        term: Sequence report
        uri: http://edamontology.org/data_2955
      format:
      - term: HTML
        uri: http://edamontology.org/format_2331
    - data:
        term: Sequence alignment (nucleic acid)
        uri: http://edamontology.org/data_1383
      format:
      - term: Binary format
        uri: http://edamontology.org/format_2333
      - term: FASTA-aln
        uri: http://edamontology.org/format_1984
  - cmd: null
    input:
    - data:
        term: Nucleic acid sequence
        uri: http://edamontology.org/data_2977
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
    note: SILVA Incremental Aligner (SINA) is used to align the rRNA gene databases
      provided by SILVA, as well as user submitted sequences. 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. Aligned sequences
      can be dowloaded as FASTA or ARB files
    operation:
    - term: Sequence alignment
      uri: http://edamontology.org/operation_0292
    output:
    - data:
        term: Sequence alignment (nucleic acid)
        uri: http://edamontology.org/data_1383
      format:
      - term: Binary format
        uri: http://edamontology.org/format_2333
      - term: FASTA-aln
        uri: http://edamontology.org/format_1984
  - cmd: null
    input:
    - data:
        term: Nucleic acid sequence
        uri: http://edamontology.org/data_2977
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
    note: SINA can also operate as a taxonomic classification tool. It uses the search
      result to derive a classification with the LCA (lowest common ancestor) method.
      Each query sequence is assigned the shared part of the classifications of the
      search results. Aligned sequences can be dowloaded as FASTA or ARB files Taxonomic
      classification results can be downloaded as csv files.
    operation:
    - term: Taxonomic classification
      uri: http://edamontology.org/operation_3460
    output:
    - data:
        term: Sequence alignment (nucleic acid)
        uri: http://edamontology.org/data_1383
      format:
      - term: Binary format
        uri: http://edamontology.org/format_2333
      - term: FASTA-aln
        uri: http://edamontology.org/format_1984
    - data:
        term: Taxonomic classification
        uri: http://edamontology.org/data_1872
      format:
      - term: Textual format
        uri: http://edamontology.org/format_2330
  - cmd: null
    input:
    - data:
        term: Nucleic acid sequence
        uri: http://edamontology.org/data_2977
      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. TestPrime 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: Textual format
        uri: http://edamontology.org/format_2330
  homepage: http://www.arb-silva.de
  homepage_status: 0
  language: []
  lastUpdate: '2025-01-22T09:59:03.064970Z'
  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
    url: https://www.arb-silva.de/aligner/
  - 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:
  - type: rrid
    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: 20831
      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: 2372
      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: 5145
      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: 2352
      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: 578
      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: 28
      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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  toolType:
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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
  version: []
- accessibility: null
  additionDate: '2016-09-30T07:30:11Z'
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    note: null
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  description: SILVAngs is a data analysis service for ribosomal RNA gene (rDNA) amplicon
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    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
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        term: Nucleic acid sequence
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    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
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        term: Nucleic acid sequence
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    - data:
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  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: 20831
      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: 2372
      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/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: 2352
      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: 10.1093/nar/gks808
    metadata:
      abstract: 16S ribosomal RNA gene (rDNA) amplicon analysis remains the standard
        approach for the cultivation-independent investigation of microbial diversity.
        The accuracy of these analyses depends strongly on the choice of primers.
        The overall coverage and phylum spectrum of 175 primers and 512 primer pairs
        were evaluated in silico with respect to the SILVA 16S/18S rDNA non-redundant
        reference dataset (SSURef 108 NR). Based on this evaluation a selection of
        'best available' primer pairs for Bacteria and Archaea for three amplicon
        size classes (100-400, 400-1000, ≥1000 bp) is provided. The most promising
        bacterial primer pair (S-D-Bact-0341-b-S-17/S-D-Bact-0785-a-A-21), with an
        amplicon size of 464 bp, was experimentally evaluated by comparing the taxonomic
        distribution of the 16S rDNA amplicons with 16S rDNA fragments from directly
        sequenced metagenomes. The results of this study may be used as a guideline
        for selecting primer pairs with the best overall coverage and phylum spectrum
        for specific applications, therefore reducing the bias in PCR-based microbial
        diversity studies. © 2012 The Author(s). Published by Oxford University Press.
      authors:
      - name: Klindworth A.
      - name: Pruesse E.
      - name: Schweer T.
      - name: Peplies J.
      - name: Quast C.
      - name: Horn M.
      - name: Glockner F.O.
      citationCount: 5992
      date: '2013-01-01T00:00:00Z'
      journal: Nucleic Acids Research
      title: Evaluation of general 16S ribosomal RNA gene PCR primers for classical
        and next-generation sequencing-based diversity studies
    note: null
    pmcid: PMC3592464
    pmid: '22933715'
    type:
    - Other
    version: null
  relation: []
  toolType:
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  topic:
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    uri: http://edamontology.org/topic_3174
  - term: Biodiversity
    uri: http://edamontology.org/topic_3050
  - term: Taxonomy
    uri: http://edamontology.org/topic_0637
  validated: 1
  version:
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- accessibility: Open access
  additionDate: '2023-08-30T13:03:57.407598Z'
  biotoolsCURIE: biotools:shic
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    fundrefid: null
    gridid: null
    name: Magnus Palmblad
    note: null
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    fundrefid: null
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    note: null
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    rorid: null
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  - email: null
    fundrefid: null
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    name: Dirk Winkelhardt
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    rorid: null
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    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Vedran Kasalica
    note: null
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    rorid: null
    typeEntity: null
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    url: null
  - email: null
    fundrefid: null
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    name: Anna-Lena Lamprecht
    note: null
    orcidid: https://orcid.org/0000-0003-1953-5606
    rorid: null
    typeEntity: null
    typeRole: []
    url: null
  description: shic is a collection of shims for use in automated workflow composition
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    - General
    url: https://github.com/magnuspalmblad/shic/README.md
  download: []
  editPermission:
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    note: null
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  - cmd: null
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  homepage: https://github.com/magnuspalmblad/shic
  homepage_status: 0
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  lastUpdate: '2025-01-16T16:39:33.218764Z'
  license: MIT
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- accessibility: Open access
  additionDate: '2024-05-05T10:53:14.688391Z'
  biotoolsCURIE: biotools:phiembed
  biotoolsID: phiembed
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  cost: Free of charge
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    fundrefid: null
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    name: Mark Edward M. Gonzales
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    url: https://a-transposable-element.com/
  description: PHIEmbed is a phage-host interaction prediction tool that uses protein
    language models to represent the receptor-binding proteins of phages. It presents
    improvements over using handcrafted (manually feature-engineered) sequence properties
    and eliminates the need to manually extract and select features from phage sequences.
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  - note: null
    type:
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    - Citation instructions
    - Command-line options
    url: https://github.com/bioinfodlsu/phage-host-prediction
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    note: Predicts the host genus of a phage given its receptor-binding protein sequences
    operation:
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  lastUpdate: '2025-01-14T09:13:55.932761Z'
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  name: PHIEmbed
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  publication:
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    metadata:
      abstract: With the growing interest in using phages to combat antimicrobial
        resistance, computational methods for predicting phage-host interactions have
        been explored to help shortlist candidate phages. Most existing models consider
        entire proteomes and rely on manual feature engineering, which poses difficulty
        in selecting the most informative sequence properties to serve as input to
        the model. In this paper, we framed phage-host interaction prediction as a
        multiclass classification problem that takes as input the embeddings of a
        phage’s receptor-binding proteins, which are known to be the key machinery
        for host recognition, and predicts the host genus. We explored different protein
        language models to automatically encode these protein sequences into dense
        embeddings without the need for additional alignment or structural information.
        We show that the use of embeddings of receptor-binding proteins presents improvements
        over handcrafted genomic and protein sequence features. The highest performance
        was obtained using the transformer-based protein language model ProtT5, resulting
        in a 3% to 4% increase in weighted F1 and recall scores across different prediction
        confidence thresholds, compared to using selected handcrafted sequence features.
      authors:
      - name: Gonzales M.E.M.
      - name: Ureta J.C.
      - name: Shrestha A.M.S.
      citationCount: 2
      date: '2023-07-01T00:00:00Z'
      journal: PLoS ONE
      title: Protein embeddings improve phage-host interaction prediction
    note: null
    pmcid: null
    pmid: '37486915'
    type:
    - Primary
    version: null
  relation: []
  toolType:
  - Command-line tool
  topic:
  - term: Machine learning
    uri: http://edamontology.org/topic_3474
  - term: Sequence analysis
    uri: http://edamontology.org/topic_0080
  - term: Proteins
    uri: http://edamontology.org/topic_0078
  - term: Proteomics
    uri: http://edamontology.org/topic_0121
  - term: Computational biology
    uri: http://edamontology.org/topic_3307
  - term: Bioinformatics
    uri: http://edamontology.org/topic_0091
  - term: Virology
    uri: http://edamontology.org/topic_0781
  validated: 0
  version: []
- accessibility: null
  additionDate: '2016-05-31T11:29:42Z'
  biotoolsCURIE: biotools:dynamine
  biotoolsID: dynamine
  collectionID: []
  confidence_flag: null
  cost: null
  credit:
  - email: null
    fundrefid: null
    gridid: null
    name: vub.ac.be
    note: null
    orcidid: null
    rorid: null
    typeEntity: Institute
    typeRole:
    - Provider
    url: null
  - email: wvranken@vub.ac.be
    fundrefid: null
    gridid: null
    name: Wim Vranken
    note: null
    orcidid: null
    rorid: null
    typeEntity: null
    typeRole:
    - Support
    url: null
  - email: wvranken@vub.ac.be
    fundrefid: null
    gridid: null
    name: Wim Vranken
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: null
  description: Protein backbone dynamics prediction from sequence.
  documentation:
  - note: null
    type:
    - General
    url: http://dynamine.ibsquare.be/help/
  download: []
  editPermission:
    authors:
    - tanish
    type: group
  elixirCommunity: []
  elixirNode: []
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  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Protein sequence (raw)
        uri: http://edamontology.org/data_2974
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
    note: Protein backbone dynamics prediction from sequence File containing one value
      per amino acid in each protein sequence
    operation:
    - term: Prediction and recognition
      uri: http://edamontology.org/operation_2423
    output:
    - data:
        term: Protein features
        uri: http://edamontology.org/data_1277
      format: []
  homepage: http://dynamine.ibsquare.be/
  homepage_status: 0
  language: []
  lastUpdate: '2025-01-08T15:03:40.105084Z'
  license: null
  link: []
  maturity: null
  name: DynaMine
  operatingSystem:
  - Linux
  - Windows
  - Mac
  otherID: []
  owner: wvranken@vub.ac.be
  publication:
  - doi: 10.1038/ncomms3741
    metadata: null
    note: null
    pmcid: null
    pmid: '24225580'
    type:
    - Other
    version: null
  - doi: 10.1093/nar/gku270
    metadata: null
    note: null
    pmcid: PMC4086073
    pmid: '24728994'
    type:
    - Other
    version: null
  relation: []
  toolType:
  - Web API
  - Web application
  topic:
  - term: Biophysics
    uri: http://edamontology.org/topic_3306
  - term: Protein properties
    uri: http://edamontology.org/topic_0123
  - term: Protein disordered structure
    uri: http://edamontology.org/topic_3538
  validated: 1
  version:
  - '1'
- accessibility: Open access
  additionDate: '2021-05-08T17:25:21Z'
  biotoolsCURIE: biotools:bakta
  biotoolsID: bakta
  collectionID: []
  confidence_flag: tool
  cost: Free of charge
  credit:
  - email: oliver.schwengers@cb.jlug.de
    fundrefid: null
    gridid: null
    name: Oliver Schwengers
    note: null
    orcidid: https://orcid.org/0000-0003-4216-2721
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    - Developer
    - Maintainer
    url: https://github.com/oschwengers
  - email: null
    fundrefid: null
    gridid: null
    name: Justus Liebig University Giessen
    note: null
    orcidid: null
    rorid: null
    typeEntity: Institute
    typeRole:
    - Provider
    url: https://www.uni-giessen.de
  description: Rapid & standardized annotation of bacterial genomes, MAGs & plasmids
  documentation:
  - note: null
    type:
    - General
    url: https://github.com/oschwengers/bakta/blob/main/README.md
  - note: null
    type:
    - Contributions policy
    url: https://github.com/oschwengers/bakta/blob/main/CONTRIBUTION.md
  - note: null
    type:
    - Code of conduct
    url: https://github.com/oschwengers/bakta/blob/main/CODE_OF_CONDUCT.md
  - note: null
    type:
    - User manual
    url: https://bakta.readthedocs.io/
  download:
  - note: Mandatory annotation database
    type: Other
    url: https://zenodo.org/records/7669534
    version: v5.1
  editPermission:
    authors:
    - ELIXIR-CZ
    - bebatut
    type: group
  elixirCommunity: []
  elixirNode:
  - Germany
  elixirPlatform:
  - Tools
  elixir_badge: 0
  function:
  - cmd: bakta --db <db-path> --prefix <prefix> --output <output-path> genome.fasta
    input:
    - data:
        term: Sequence assembly
        uri: http://edamontology.org/data_0925
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
    - data:
        term: Sequence features metadata
        uri: http://edamontology.org/data_2914
      format:
      - term: TSV
        uri: http://edamontology.org/format_3475
    - data:
        term: Sequence coordinates
        uri: http://edamontology.org/data_2012
      format:
      - term: GFF3
        uri: http://edamontology.org/format_1975
    - data:
        term: Protein sequence record
        uri: http://edamontology.org/data_2886
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
    - data:
        term: Hidden Markov model
        uri: http://edamontology.org/data_1364
      format:
      - term: HMMER3
        uri: http://edamontology.org/format_3329
    note: null
    operation:
    - term: Genome annotation
      uri: http://edamontology.org/operation_0362
    output:
    - data:
        term: Feature table
        uri: http://edamontology.org/data_1270
      format:
      - term: GenBank format
        uri: http://edamontology.org/format_1936
      - term: EMBL format
        uri: http://edamontology.org/format_1927
      - term: GFF3
        uri: http://edamontology.org/format_1975
      - term: JSON
        uri: http://edamontology.org/format_3464
      - term: TSV
        uri: http://edamontology.org/format_3475
    - data:
        term: Protein sequence record
        uri: http://edamontology.org/data_2886
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
    - data:
        term: Nucleic acid sequence record
        uri: http://edamontology.org/data_2887
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
    - data:
        term: Plot
        uri: http://edamontology.org/data_2884
      format:
      - term: PNG
        uri: http://edamontology.org/format_3603
      - term: SVG
        uri: http://edamontology.org/format_3604
    - data:
        term: Score
        uri: http://edamontology.org/data_1772
      format:
      - term: TSV
        uri: http://edamontology.org/format_3475
  homepage: https://github.com/oschwengers/bakta
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2024-12-23T21:48:50.049892Z'
  license: GPL-3.0
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/oschwengers/bakta
  - note: null
    type:
    - Issue tracker
    url: https://github.com/oschwengers/bakta/issues
  - note: null
    type:
    - Other
    url: https://bioconda.github.io/recipes/bakta/README.html
  - note: null
    type:
    - Service
    url: https://bakta.computational.bio
  maturity: Mature
  name: Bakta
  operatingSystem:
  - Linux
  - Mac
  otherID: []
  owner: oschwengers
  publication:
  - doi: 10.1099/mgen.0.000685
    metadata:
      abstract: Command-line annotation software tools have continuously gained popularity
        compared to centralized online services due to the worldwide increase of sequenced
        bacterial genomes. However, results of existing command-line software pipelines
        heavily depend on taxon-specific databases or sufficiently well annotated
        reference genomes. Here, we introduce Bakta, a new command-line software tool
        for the robust, taxon-independent, thorough and, nonetheless, fast annotation
        of bacterial genomes. Bakta conducts a comprehensive annotation workflow including
        the detection of small proteins taking into account replicon metadata. The
        annotation of coding sequences is accelerated via an alignment-free sequence
        identification approach that in addition facilitates the precise assignment
        of public database cross-references. Annotation results are exported in GFF3
        and International Nucleotide Sequence Database Collaboration (INSDC)-compliant
        flat files, as well as comprehensive JSON files, facilitating automated downstream
        analysis. We compared Bakta to other rapid contemporary command-line annotation
        software tools in both targeted and taxonomically broad benchmarks including
        isolates and metagenomic-assembled genomes. We demonstrated that Bakta outperforms
        other tools in terms of functional annotations, the assignment of functional
        categories and database cross-references, whilst providing comparable wall-clock
        runtimes. Bakta is implemented in Python 3 and runs on MacOS and Linux systems.
        It is freely available under a GPLv3 license at https://​github.​com/​oschwengers/​bakta.
        An accompanying web version is available at https://​bakta.​computational.​bio.
      authors:
      - name: Schwengers O.
      - name: Jelonek L.
      - name: Dieckmann M.A.
      - name: Beyvers S.
      - name: Blom J.
      - name: Goesmann A.
      citationCount: 323
      date: '2021-01-01T00:00:00Z'
      journal: Microbial Genomics
      title: 'Bakta: Rapid and standardized annotation of bacterial genomes via alignment-free
        sequence identification'
    note: null
    pmcid: PMC8743544
    pmid: '34739369'
    type:
    - Primary
    version: '1.1'
  relation:
  - biotoolsID: diamond
    type: uses
  - biotoolsID: hmmer3
    type: uses
  - biotoolsID: infernal
    type: uses
  - biotoolsID: trnascan-se
    type: uses
  - biotoolsID: blast
    type: uses
  - biotoolsID: aragorn
    type: uses
  - biotoolsID: pilercr
    type: uses
  - biotoolsID: deepsig
    type: uses
  toolType:
  - Command-line tool
  - Web application
  topic:
  - term: Genomics
    uri: http://edamontology.org/topic_0622
  - term: Sequence analysis
    uri: http://edamontology.org/topic_0080
  - term: Bioinformatics
    uri: http://edamontology.org/topic_0091
  validated: 0
  version:
  - v1.10.3
- 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: 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 program for multiple sequence alignment editing,
    visualisation and analysis. Use it to 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
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Sequence alignment
        uri: http://edamontology.org/data_0863
      format:
      - term: GFF3-seq
        uri: http://edamontology.org/format_1939
      - term: ClustalW format
        uri: http://edamontology.org/format_1982
      - term: Stockholm format
        uri: http://edamontology.org/format_1961
      - term: FASTA-aln
        uri: http://edamontology.org/format_1984
      - term: GFF2-seq
        uri: http://edamontology.org/format_1938
      - term: FASTA
        uri: http://edamontology.org/format_1929
      - term: nbrf/pir
        uri: http://edamontology.org/format_1948
      - term: BioJSON (Jalview)
        uri: http://edamontology.org/format_3774
      - term: PHYLIP format
        uri: http://edamontology.org/format_1997
      - term: BLC
        uri: http://edamontology.org/format_3313
      - term: RNAML
        uri: http://edamontology.org/format_3311
      - term: GCG MSF
        uri: http://edamontology.org/format_1947
      - term: Pileup
        uri: http://edamontology.org/format_3015
      - term: mmCIF
        uri: http://edamontology.org/format_1477
      - term: VCF
        uri: http://edamontology.org/format_3016
      - term: Format
        uri: http://edamontology.org/format_1915
    - data:
        term: Structure alignment
        uri: http://edamontology.org/data_0886
      format:
      - term: PDB
        uri: http://edamontology.org/format_1476
    note: 'Other Input formats:

      AMSA (.amsa);

      JnetFile (.concise, .jnet);

      PFAM (.pfam);

      Substitution matrix (.matrix);

      Jalview Project File (.jvp);

      Jalview Feature File (.features, .jvfeatures);

      Jalview Annotations File (.annotations, .jvannotations);

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

      ...

      Other Output formats:

      PFAM (.pfam);

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

      Jalview Project File (.jvp);'
    operation:
    - term: Sequence visualisation
      uri: http://edamontology.org/operation_0564
    - term: Phylogenetic tree analysis
      uri: http://edamontology.org/operation_0324
    - term: Sequence alignment editing
      uri: http://edamontology.org/operation_3081
    output:
    - data:
        term: Sequence alignment
        uri: http://edamontology.org/data_0863
      format:
      - term: nbrf/pir
        uri: http://edamontology.org/format_1948
      - term: JSON
        uri: http://edamontology.org/format_3464
      - term: Stockholm format
        uri: http://edamontology.org/format_1961
      - term: FASTA
        uri: http://edamontology.org/format_1929
      - term: PHYLIP format
        uri: http://edamontology.org/format_1997
      - term: BLC
        uri: http://edamontology.org/format_3313
      - term: BioJSON (Jalview)
        uri: http://edamontology.org/format_3774
      - term: GCG MSF
        uri: http://edamontology.org/format_1947
      - term: Pileup
        uri: http://edamontology.org/format_3015
      - term: ClustalW format
        uri: http://edamontology.org/format_1982
    - data:
        term: Plot
        uri: http://edamontology.org/data_2884
      format:
      - term: PNG
        uri: http://edamontology.org/format_3603
      - term: HTML
        uri: http://edamontology.org/format_2331
      - term: EPS
        uri: http://edamontology.org/format_3466
      - term: SVG
        uri: http://edamontology.org/format_3604
      - term: Format
        uri: http://edamontology.org/format_1915
  homepage: https://www.jalview.org/
  homepage_status: 0
  language: []
  lastUpdate: '2024-11-28T10:07:42.658684Z'
  license: GPL-3.0
  link:
  - note: null
    type:
    - Discussion forum
    url: https://discourse.jalview.org/
  - note: null
    type:
    - Issue tracker
    url: https://issues.jalview.org/
  - note: Latest development version
    type:
    - Other
    url: https://www.jalview.org/development/jalview_develop/
  - note: null
    type:
    - Repository
    url: https://source.jalview.org/crucible/browse/jalview
  - note: Twitter feed
    type:
    - Social media
    url: https://twitter.com/Jalview
  - note: YouTube training videos
    type:
    - Social media
    url: https://www.youtube.com/channel/UCIjpnvZB770yz7ftbrJ0tfw
  maturity: Mature
  name: Jalview
  operatingSystem:
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  - Windows
  - Mac
  otherID: []
  owner: ben_s
  publication:
  - doi: 10.1093/bioinformatics/btp033
    metadata: null
    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
  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:
  - 2.11.4.1
- accessibility: Open access
  additionDate: '2019-07-03T16:03:27Z'
  biotoolsCURIE: biotools:MMseqs2
  biotoolsID: MMseqs2
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit: []
  description: 'MMseqs2 (Many-against-Many sequence searching) is a software suite
    to search and cluster huge protein and nucleotide sequence sets. MMseqs2 is open
    source GPL-licensed software implemented in C++ for Linux, MacOS, and (as beta
    version, via cygwin) Windows. The software is designed to run on multiple cores
    and servers and exhibits very good scalability. MMseqs2 can run 10000 times faster
    than BLAST. At 100 times its speed it achieves almost the same sensitivity. It
    can perform profile searches with the same sensitivity as PSI-BLAST at over 400
    times its speed.


    MMseqs2 includes Linclust, the first clustering algorithm whose runtime scales
    linearly With Linclust we clustered 1.6 billion metagenomic sequence fragments
    in 10 h on a single server to 50% sequence identity.'
  documentation:
  - note: null
    type:
    - General
    url: https://github.com/soedinglab/MMseqs2/blob/master/README.md
  - note: null
    type:
    - User manual
    url: https://github.com/soedinglab/mmseqs2/wiki
  - note: Tutorial material
    type:
    - Training material
    url: https://github.com/soedinglab/MMseqs2/wiki/Tutorials
  download:
  - note: null
    type: Source code
    url: https://github.com/soedinglab/MMseqs2/releases
    version: null
  editPermission:
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  elixirNode: []
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  elixir_badge: 0
  function:
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    input:
    - data:
        term: Sequence set
        uri: http://edamontology.org/data_0850
      format:
      - term: FASTQ-like format (text)
        uri: http://edamontology.org/format_2182
      - term: FASTA-like (text)
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    note: null
    operation:
    - term: Sequence similarity search
      uri: http://edamontology.org/operation_0346
    - term: Sequence alignment
      uri: http://edamontology.org/operation_0292
    output:
    - data:
        term: Sequence search results
        uri: http://edamontology.org/data_0857
      format:
      - term: BLAST results
        uri: http://edamontology.org/format_1333
  - cmd: 'mmseqs easy-cluster input.fasta output tmp

      mmseqs easy-linclust input.fasta output tmp'
    input:
    - data:
        term: Sequence set
        uri: http://edamontology.org/data_0850
      format:
      - term: FASTQ-like format (text)
        uri: http://edamontology.org/format_2182
      - term: FASTA-like (text)
        uri: http://edamontology.org/format_2200
    note: null
    operation:
    - term: Sequence clustering
      uri: http://edamontology.org/operation_0291
    output:
    - data:
        term: Sequence cluster
        uri: http://edamontology.org/data_1235
      format: []
  - cmd: mmseqs easy-taxonomy query.fasta targetDB output tmp
    input:
    - data:
        term: Sequence set
        uri: http://edamontology.org/data_0850
      format:
      - term: FASTQ-like format (text)
        uri: http://edamontology.org/format_2182
      - term: FASTA-like (text)
        uri: http://edamontology.org/format_2200
    note: null
    operation:
    - term: Taxonomic classification
      uri: http://edamontology.org/operation_3460
    output:
    - data:
        term: Taxonomy
        uri: http://edamontology.org/data_3028
      format: []
  homepage: https://mmseqs.com
  homepage_status: 0
  language:
  - C++
  lastUpdate: '2024-11-26T16:25:05.809769Z'
  license: MIT
  link:
  - note: null
    type:
    - Issue tracker
    url: https://github.com/soedinglab/mmseqs2/issues
  - note: null
    type:
    - Repository
    url: https://github.com/soedinglab/mmseqs2
  maturity: Mature
  name: MMseqs2
  operatingSystem:
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  - Windows
  - Mac
  otherID: []
  owner: milot-mirdita
  publication:
  - doi: 10.1038/nbt.3988
    metadata: null
    note: null
    pmcid: null
    pmid: '29035372'
    type: []
    version: null
  - doi: 10.1101/079681
    metadata: null
    note: null
    pmcid: null
    pmid: null
    type: []
    version: null
  - doi: 10.1038/s41467-018-04964-5
    metadata: null
    note: null
    pmcid: PMC6026198
    pmid: '29959318'
    type:
    - Method
    version: null
  - doi: 10.1093/bioinformatics/bty1057
    metadata: null
    note: null
    pmcid: PMC6691333
    pmid: '30615063'
    type:
    - Method
    version: null
  - doi: 10.1101/2020.11.27.401018
    metadata: null
    note: null
    pmcid: null
    pmid: null
    type: []
    version: null
  - doi: 10.1093/bioinformatics/btab184
    metadata: null
    note: MMseqs2 Taxonomy
    pmcid: PMC8479651
    pmid: '33734313'
    type: []
    version: null
  - doi: 10.1101/2024.11.13.623350v1
    metadata: null
    note: MMseqs2-GPU
    pmcid: null
    pmid: null
    type: []
    version: null
  relation:
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    type: includes
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    type: usedBy
  - biotoolsID: conterminator
    type: usedBy
  - biotoolsID: spacepharer
    type: usedBy
  toolType:
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  topic:
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    uri: http://edamontology.org/topic_3174
  - term: Sequence analysis
    uri: http://edamontology.org/topic_0080
  - term: Proteins
    uri: http://edamontology.org/topic_0078
  - term: Nucleic acids
    uri: http://edamontology.org/topic_0077
  - term: Gene and protein families
    uri: http://edamontology.org/topic_0623
  - term: Taxonomy
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  validated: 1
  version: []
- accessibility: null
  additionDate: '2015-08-24T10:00:36Z'
  biotoolsCURIE: biotools:cofactory
  biotoolsID: cofactory
  collectionID: []
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    note: null
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    url: null
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    url: null
  description: Identification of Rossmann folds and prediction of FAD, NAD and NADP
    specificity.
  documentation:
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    url: http://www.cbs.dtu.dk/services/Cofactory/instructions.php
  download:
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    version: null
  - note: null
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    version: null
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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: identifies Rossmann fold sequence domains and predicts their specificity
      for the cofactors FAD, NAD or NADP
    operation:
    - term: Prediction and recognition
      uri: http://edamontology.org/operation_2423
    output:
    - data:
        term: Protein features
        uri: http://edamontology.org/data_1277
      format:
      - term: Textual format
        uri: http://edamontology.org/format_2330
  homepage: http://cbs.dtu.dk/services/Cofactory/
  homepage_status: 0
  language: []
  lastUpdate: '2024-11-25T16:22:09.216410Z'
  license: Other
  link:
  - note: null
    type:
    - Repository
    url: http://www.cbs.dtu.dk/services/doc/cofactory-1.0.readme
  - note: null
    type:
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    url: http://cbs.dtu.dk/services
  maturity: Emerging
  name: Cofactory
  operatingSystem:
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  otherID: []
  owner: CBS
  publication:
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    metadata: null
    note: null
    pmcid: null
    pmid: '24523134'
    type:
    - Primary
    version: null
  relation: []
  toolType:
  - Web application
  topic:
  - term: Protein sites, features and motifs
    uri: http://edamontology.org/topic_3510
  validated: 1
  version:
  - '2.1'
- accessibility: null
  additionDate: '2016-06-02T02:47:10Z'
  biotoolsCURIE: biotools:msa
  biotoolsID: msa
  collectionID:
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  - BioJS
  confidence_flag: null
  cost: Free of charge
  credit:
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    fundrefid: null
    gridid: null
    name: Sebastian Wilzbach
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
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    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Ian Sillitoe
    note: null
    orcidid: null
    rorid: null
    typeEntity: null
    typeRole:
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    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Guy Yachdav
    note: null
    orcidid: null
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    typeEntity: null
    typeRole:
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    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Benedikt Rauscher
    note: null
    orcidid: null
    rorid: null
    typeEntity: null
    typeRole:
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    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:
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    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:
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    url: null
  - email: null
    fundrefid: null
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    note: null
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    rorid: null
    typeEntity: Institute
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    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: null
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
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    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:
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    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
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    url: https://github.com/wilzbach/msa
    version: null
  - note: null
    type: Binaries
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    version: null
  editPermission:
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  elixirCommunity: []
  elixirNode: []
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  elixir_badge: 0
  function:
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    input:
    - data:
        term: Sequence alignment
        uri: http://edamontology.org/data_0863
      format:
      - term: ClustalW format
        uri: http://edamontology.org/format_1982
      - term: FASTA-aln
        uri: http://edamontology.org/format_1984
    note: 'Visualizes multiple sequence alignment, calculates conservation, shows
      sequence logo, applies multiple color schemes A multiple sequence alignment
      (ClustalW, FASTA, ...) Exports selected sequences and regions from the alignment
      Images are exported in PNG Export sequences in FASTA format Export features
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      NOTE: Actually, all these output types of data should instead be under separate
      "constant" operations, while the visualisation should be an unary operation,
      perhaps without an output.'
    operation:
    - term: Sequence visualisation
      uri: http://edamontology.org/operation_0564
    output:
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      format:
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        uri: http://edamontology.org/format_1984
    - data:
        term: Sequence alignment image
        uri: http://edamontology.org/data_1711
      format:
      - term: Image format
        uri: http://edamontology.org/format_3547
    - data:
        term: Sequence set
        uri: http://edamontology.org/data_0850
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
    - data:
        term: Feature table
        uri: http://edamontology.org/data_1270
      format:
      - term: GFF
        uri: http://edamontology.org/format_2305
  - cmd: null
    input:
    - data:
        term: Nucleic acid sequence
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      - term: FASTA
        uri: http://edamontology.org/format_1929
      - term: GCG
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      - term: PHYLIP format
        uri: http://edamontology.org/format_1997
      - term: EMBL format
        uri: http://edamontology.org/format_1927
      - term: GenBank format
        uri: http://edamontology.org/format_1936
    - data:
        term: Protein sequence
        uri: http://edamontology.org/data_2976
      format:
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        uri: http://edamontology.org/format_1948
      - term: FASTA
        uri: http://edamontology.org/format_1929
      - term: GCG
        uri: http://edamontology.org/format_1935
      - term: PHYLIP format
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      - term: EMBL format
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      - term: GenBank format
        uri: http://edamontology.org/format_1936
    note: null
    operation:
    - term: Multiple sequence alignment
      uri: http://edamontology.org/operation_0492
    output:
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      format:
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      - term: FASTA
        uri: http://edamontology.org/format_1929
      - term: PHYLIP format
        uri: http://edamontology.org/format_1997
      - term: PDF
        uri: http://edamontology.org/format_3508
  homepage: http://msa.biojs.net
  homepage_status: 0
  language:
  - JavaScript
  lastUpdate: '2024-11-25T16:17:03.898741Z'
  license: Apache-2.0
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/wilzbach/msa
  - note: null
    type:
    - Software catalogue
    url: http://biojs.io/
  - note: null
    type:
    - Helpdesk
    url: http://github.com/wilzbach/msa
  - note: null
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  maturity: Mature
  name: msa
  operatingSystem:
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  - Windows
  - Mac
  otherID: []
  owner: BioJS
  publication:
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    metadata: null
    note: null
    pmcid: PMC5181560
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    type:
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    version: null
  - doi: 10.1093/bioinformatics/btv494
    metadata: null
    note: null
    pmcid: null
    pmid: '26315911'
    type:
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    version: null
  relation: []
  toolType:
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  - Library
  topic:
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    uri: http://edamontology.org/topic_0080
  - term: Sequence sites, features and motifs
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  - term: Phylogenetics
    uri: http://edamontology.org/topic_3293
  - term: Sequencing
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  validated: 1
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- accessibility: null
  additionDate: '2015-01-21T15:12:23Z'
  biotoolsCURIE: biotools:crispi
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    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
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  description: A CRISPR Interactive database.
  documentation:
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  download: []
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  function:
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      format:
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    note: A CRISPR Interactive database
    operation:
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    output:
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      format:
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  homepage: http://crispi.genouest.org/
  homepage_status: 0
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  license: null
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    metadata: null
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    pmcid: PMC2788928
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    type:
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  relation: []
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  description: A heterogeneous ensemble algorithm which is the voting of multi-expert
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  description: Algorithm for genome scaffoldin which exploits information obtained
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  description: Simple tool based on the iterative mapping of sequence reads at contig
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  description: R package for the study of prokaryotic pan-genomes. A pan-genome is
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    - data:
        term: DNA sequence (raw)
        uri: http://edamontology.org/data_3497
      format:
      - term: FASTA-like
        uri: http://edamontology.org/format_2546
    note: null
    operation:
    - term: Classification
      uri: http://edamontology.org/operation_2990
    output:
    - data:
        term: Phylogenetic tree
        uri: http://edamontology.org/data_0872
      format: []
  homepage: https://cran.r-project.org/web/packages/micropan/index.html
  homepage_status: 0
  language:
  - R
  lastUpdate: '2024-11-25T15:40:41.292532Z'
  license: GPL-2.0
  link: []
  maturity: Mature
  name: micropan
  operatingSystem:
  - Linux
  - Windows
  - Mac
  otherID: []
  owner: UiO
  publication:
  - doi: 10.1186/s12859-015-0517-0
    metadata: null
    note: null
    pmcid: PMC4375852
    pmid: '25888166'
    type:
    - Primary
    version: null
  relation: []
  toolType:
  - Command-line tool
  topic:
  - term: Biology
    uri: http://edamontology.org/topic_3070
  - term: Microbiology
    uri: http://edamontology.org/topic_3301
  - term: Comparative genomics
    uri: http://edamontology.org/topic_0797
  validated: 1
  version:
  - '1.0'
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