count: 428
list:
- accessibility: Open access
  additionDate: '2025-12-15T14:17:14.627791Z'
  biotoolsCURIE: biotools:asafind
  biotoolsID: asafind
  collectionID:
  - ELIXIR-CZ
  - Czech Republic
  confidence_flag: tool
  cost: Free of charge
  credit:
  - email: mvohnoutova@jcu.cz
    fundrefid: null
    gridid: null
    name: Marta Vohnoutová
    note: null
    orcidid: https://orcid.org/0000-0002-8915-8626
    rorid: null
    typeEntity: Person
    typeRole:
    - Contributor
    - Developer
    - Maintainer
    url: https://www.jcu.cz/cz/univerzita/lide/clovek?identita=Vohnoutova_Marta_61699
  - email: agruber@prf.jcu.cz
    fundrefid: null
    gridid: null
    name: Ansgar Gruber
    note: null
    orcidid: https://orcid.org/0000-0002-5876-4391
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    - Developer
    - Documentor
    url: https://www.jcu.cz/cz/univerzita/lide/clovek?identita=Gruber_Ansgar_118401
  description: "ASAFind is a software that predicts the intracellular location of\
    \ proteins in cells with four membrane-bound complex plastids of red algal origin.\
    \ \nThese plastids evolved via eukaryote-eukaryote endosymbiosis and for example\
    \ can be found in diatoms and cryptophytes. ASAFind uses protein sequence data\
    \ and external predictions of signal peptides (by the tools SignalP and TargetP),\
    \ and predicts plastid proteins, and proteins that are targeted to the periplastidic\
    \ compartment from these data; optionally, a graphical output can generated."
  documentation:
  - note: null
    type:
    - Installation instructions
    url: https://asafind.jcu.cz/download-page/
  download:
  - note: Download page on web-service, links to repository
    type: Downloads page
    url: https://asafind.jcu.cz/download-page/
    version: '2.0'
  editPermission:
    authors:
    - agruber
    type: group
  elixirCommunity:
  - Plant Sciences
  - Marine Metagenomics
  - Microbial Biotechnology
  elixirNode:
  - Czech Republic
  elixirPlatform:
  - Tools
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Protein sequence record
        uri: http://edamontology.org/data_2886
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
    - data:
        term: Feature table
        uri: http://edamontology.org/data_1270
      format: []
    note: null
    operation:
    - term: Subcellular localisation prediction
      uri: http://edamontology.org/operation_2489
    - term: Sequence motif recognition
      uri: http://edamontology.org/operation_0239
    - term: Protein cleavage site prediction
      uri: http://edamontology.org/operation_0422
    output:
    - data:
        term: Protein features
        uri: http://edamontology.org/data_1277
      format: []
    - data:
        term: Plot
        uri: http://edamontology.org/data_2884
      format: []
  homepage: https://asafind.jcu.cz/
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2025-12-15T17:36:43.189214Z'
  license: CC-BY-SA-4.0
  link:
  - note: Web Service
    type:
    - Service
    url: https://asafind.jcu.cz
  - note: Information and source code, for local installation or development
    type:
    - Repository
    url: https://github.com/ASAFind/ASAFind-2
  maturity: Mature
  name: ASAFind
  operatingSystem:
  - Mac
  - Linux
  otherID: []
  owner: martavohnoutova
  publication:
  - doi: 10.1111/tpj.70138
    metadata:
      abstract: ''
      authors: []
      citationCount: 0
      date: '2025-06-01T00:00:00Z'
      journal: Plant Journal
      title: 'ASAFind 2.0: multi-class protein targeting prediction for diatoms and
        algae with complex plastids'
    note: Publication of the current version of ASAFind (2.0)
    pmcid: PMC12136025
    pmid: '40464854'
    type:
    - Primary
    version: '2.0'
  - doi: 10.1111/tpj.12734
    metadata:
      abstract: ''
      authors: []
      citationCount: 138
      date: '2015-02-01T00:00:00Z'
      journal: Plant Journal
      title: Plastid proteome prediction for diatoms and other algae with secondary
        plastids of the red lineage
    note: Publication of the first version of ASAFind
    pmcid: PMC4329603
    pmid: '25438865'
    type:
    - Other
    version: '1.0'
  - doi: 10.48550/arXiv.2303.02509
    metadata: null
    note: Benchmarking of the performance of the first version of ASAFind
    pmcid: null
    pmid: null
    type:
    - Benchmarking study
    version: '1.0'
  relation:
  - biotoolsID: signalp
    type: uses
  - biotoolsID: targetp
    type: uses
  toolType:
  - Script
  - Command-line tool
  - Web service
  topic:
  - term: Cell biology
    uri: http://edamontology.org/topic_2229
  - term: Proteins
    uri: http://edamontology.org/topic_0078
  - term: Plant biology
    uri: http://edamontology.org/topic_0780
  - term: Genomics
    uri: http://edamontology.org/topic_0622
  validated: 0
  version:
  - '2.0'
- accessibility: Open access (with restrictions)
  additionDate: '2025-12-09T09:22:22.735091Z'
  biotoolsCURIE: biotools:instanovo
  biotoolsID: instanovo
  collectionID:
  - proteomics
  - ms-utils
  confidence_flag: null
  cost: Free of charge (with restrictions)
  credit:
  - email: k.eloff@instadeep.com
    fundrefid: null
    gridid: null
    name: Kevin Eloff
    note: null
    orcidid: https://orcid.org/0000-0003-1355-8743
    rorid: null
    typeEntity: null
    typeRole:
    - Primary contact
    url: null
  - email: konka@dtu.dk
    fundrefid: null
    gridid: null
    name: Konstantinos Kalogeropoulos
    note: null
    orcidid: https://orcid.org/0000-0003-3907-9281
    rorid: null
    typeEntity: null
    typeRole:
    - Primary contact
    url: null
  - email: r.catzel@instadeep.com
    fundrefid: null
    gridid: null
    name: Rachel Catzel
    note: null
    orcidid: https://orcid.org/0000-0002-2983-9833
    rorid: null
    typeEntity: null
    typeRole:
    - Maintainer
    url: null
  - email: j.vangoey@instadeep.com
    fundrefid: null
    gridid: null
    name: Jeroen Van Goey
    note: null
    orcidid: https://orcid.org/0000-0003-4480-5567
    rorid: null
    typeEntity: null
    typeRole:
    - Maintainer
    url: null
  - email: tpaje@dtu.dk
    fundrefid: null
    gridid: null
    name: Timothy P. Jenkins
    note: null
    orcidid: https://orcid.org/0000-0003-2979-5663
    rorid: null
    typeEntity: null
    typeRole:
    - Support
    url: null
  description: InstaNovo is a transformer neural network with the ability to translate
    fragment ion peaks into the sequence of amino acids that make up the studied peptide(s).
  documentation:
  - note: null
    type:
    - General
    url: https://instadeepai.github.io/InstaNovo/
  - note: null
    type:
    - Installation instructions
    url: https://instadeepai.github.io/InstaNovo/tutorials/getting_started/#installation
  - note: null
    type:
    - Quick start guide
    url: https://instadeepai.github.io/InstaNovo/tutorials/getting_started/
  - note: null
    type:
    - Command-line options
    url: https://instadeepai.github.io/InstaNovo/reference/cli/
  - note: null
    type:
    - API documentation
    url: https://instadeepai.github.io/InstaNovo/API/summary/
  - note: null
    type:
    - Citation instructions
    url: https://instadeepai.github.io/InstaNovo/citation/
  download:
  - note: null
    type: Source code
    url: https://github.com/instadeepai/InstaNovo/releases/tag/1.2.2
    version: 1.1.2
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: instanovo predict --data-path /path/to/your/spectra.mgf --output-path predictions.csv
    input:
    - data:
        term: Mass spectrum
        uri: http://edamontology.org/data_0943
      format:
      - term: mzML
        uri: http://edamontology.org/format_3244
      - term: mzXML
        uri: http://edamontology.org/format_3654
      - term: MGF
        uri: http://edamontology.org/format_3651
    note: null
    operation:
    - term: de Novo sequencing
      uri: http://edamontology.org/operation_3644
    output:
    - data:
        term: Protein sequence record
        uri: http://edamontology.org/data_2886
      format:
      - term: CSV
        uri: http://edamontology.org/format_3752
  homepage: https://github.com/instadeepai/instanovo
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2025-12-09T21:41:17.117080Z'
  license: Apache-2.0
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/instadeepai/instanovo
  - note: null
    type:
    - Other
    url: https://instanovo.ai/
  - note: null
    type:
    - Issue tracker
    url: https://github.com/instadeepai/InstaNovo/issues
  - note: null
    type:
    - Discussion forum
    url: https://github.com/instadeepai/InstaNovo/discussions
  maturity: Mature
  name: InstaNovo
  operatingSystem:
  - Windows
  - Mac
  - Linux
  otherID: []
  owner: BioGeek
  publication:
  - doi: 10.1038/s42256-025-01019-5
    metadata:
      abstract: ''
      authors: []
      citationCount: 7
      date: '2025-04-01T00:00:00Z'
      journal: Nature Machine Intelligence
      title: InstaNovo enables diffusion-powered de novo peptide sequencing in large-scale
        proteomics experiments
    note: null
    pmcid: null
    pmid: null
    type:
    - Primary
    version: 1.1.4
  relation:
  - biotoolsID: matchms
    type: uses
  - biotoolsID: pyteomics
    type: uses
  - biotoolsID: spectrum_utils
    type: uses
  toolType:
  - Command-line tool
  topic:
  - term: Proteomics
    uri: http://edamontology.org/topic_0121
  - term: Proteins
    uri: http://edamontology.org/topic_0078
  - term: Proteomics experiment
    uri: http://edamontology.org/topic_3520
  - term: Machine learning
    uri: http://edamontology.org/topic_3474
  validated: 0
  version:
  - 1.2.2
- 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: HTML
        uri: http://edamontology.org/format_2331
      - term: PDF
        uri: http://edamontology.org/format_3508
  homepage: https://github.com/prolfqua/prolfquapp
  homepage_status: 0
  language:
  - R
  lastUpdate: '2025-11-06T14:37:12.116175Z'
  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: ''
      authors: []
      citationCount: 1
      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:
    - Primary
    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: '2016-10-20T10:31:19Z'
  biotoolsCURIE: biotools:peptideshaker
  biotoolsID: peptideshaker
  collectionID:
  - de.NBI
  - Proteomics
  - BioInfra.Prot
  confidence_flag: null
  cost: null
  credit:
  - email: null
    fundrefid: null
    gridid: null
    name: BioInfra.Prot
    note: null
    orcidid: null
    rorid: null
    typeEntity: Institute
    typeRole:
    - Provider
    url: null
  - email: dominik.kopczynski@isas.de
    fundrefid: null
    gridid: null
    name: Dominik Kopczynsk
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: http://compomics.github.io/projects/peptide-shaker.html
  description: PeptideShaker is a search engine independent platform for interpretation
    of proteomics identification results from multiple search engines, currently supporting
    X!Tandem, MS-GF+, MS Amanda, OMSSA, MyriMatch, Comet, Tide, Mascot, Andromeda
    and mzIdentML. By combining the results from multiple search engines, while re-calculating
    PTM localization scores and redoing the protein inference, PeptideShaker attempts
    to give you the best possible understanding of your proteomics data
  documentation:
  - note: null
    type:
    - General
    url: http://compomics.github.io/projects/peptide-shaker.html#read-me
  download:
  - note: null
    type: Source code
    url: https://github.com/compomics/peptide-shaker
    version: null
  editPermission:
    authors:
    - proteomics.bio.tools
    - veits@bmb.sdu.dk
    type: group
  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
    - data:
        term: Peptide identification
        uri: http://edamontology.org/data_0945
      format:
      - term: mzIdentML
        uri: http://edamontology.org/format_3247
    - data:
        term: Mass spectrometry data
        uri: http://edamontology.org/data_2536
      format:
      - term: MGF
        uri: http://edamontology.org/format_3651
    note: null
    operation:
    - term: Mass spectrum visualisation
      uri: http://edamontology.org/operation_3694
    - term: Peptide identification
      uri: http://edamontology.org/operation_3631
    - term: Validation
      uri: http://edamontology.org/operation_2428
    - term: PTM localisation
      uri: http://edamontology.org/operation_3755
    - term: Enrichment analysis
      uri: http://edamontology.org/operation_3501
    - term: Structure visualisation
      uri: http://edamontology.org/operation_0570
    - term: Protein identification
      uri: http://edamontology.org/operation_3767
    output:
    - data:
        term: Protein structure image
        uri: http://edamontology.org/data_2992
      format:
      - term: JPG
        uri: http://edamontology.org/format_3579
      - term: SVG
        uri: http://edamontology.org/format_3604
    - data:
        term: GO-term enrichment data
        uri: http://edamontology.org/data_3754
      format:
      - term: Textual format
        uri: http://edamontology.org/format_2330
    - data:
        term: Sequence image
        uri: http://edamontology.org/data_2969
      format:
      - term: Image format
        uri: http://edamontology.org/format_3547
    - data:
        term: Protein report
        uri: http://edamontology.org/data_0896
      format:
      - term: TSV
        uri: http://edamontology.org/format_3475
  homepage: http://compomics.github.io/projects/peptide-shaker.html
  homepage_status: 0
  language:
  - Java
  lastUpdate: '2025-11-01T15:59:45.423975Z'
  license: Apache-2.0
  link: []
  maturity: null
  name: PeptideShaker
  operatingSystem:
  - Mac
  - Linux
  otherID: []
  owner: BioInfra.Prot
  publication:
  - doi: 10.1038/nbt.3109
    metadata:
      abstract: ''
      authors: []
      citationCount: 449
      date: '2015-01-01T00:00:00Z'
      journal: Nature Biotechnology
      title: 'PeptideShaker enables reanalysis of MS-derived proteomics data sets:
        To the editor'
    note: null
    pmcid: null
    pmid: '25574629'
    type:
    - Primary
    version: null
  relation: []
  toolType:
  - Desktop application
  - Command-line tool
  topic:
  - term: Proteomics
    uri: http://edamontology.org/topic_0121
  - term: Proteomics experiment
    uri: http://edamontology.org/topic_3520
  - term: Proteome
    uri: http://edamontology.org/topic_0644
  validated: 1
  version:
  - 3.0.11
- accessibility: null
  additionDate: '2025-10-29T16:12:04.796577Z'
  biotoolsCURIE: biotools:ngp
  biotoolsID: ngp
  collectionID: []
  confidence_flag: null
  cost: null
  credit: []
  description: Simulation of next-generation proteomics (NGP) based on single-molecule
    sequencing.
  documentation: []
  download: []
  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: Modelling and simulation
      uri: http://edamontology.org/operation_2426
    output:
    - data:
        term: Simulation
        uri: http://edamontology.org/data_3869
      format:
      - term: CSV
        uri: http://edamontology.org/format_3752
      - term: PDF
        uri: http://edamontology.org/format_3508
  homepage: https://github.com/magnuspalmblad/NGP
  homepage_status: 0
  language: []
  lastUpdate: '2025-10-29T16:12:04.798957Z'
  license: null
  link: []
  maturity: null
  name: NGP
  operatingSystem: []
  otherID: []
  owner: n.m.palmblad@lumc.nl
  publication:
  - doi: 10.1021/acs.jproteome.1c00136
    metadata:
      abstract: ''
      authors: []
      citationCount: 5
      date: '2021-06-04T00:00:00Z'
      journal: Journal of Proteome Research
      title: Theoretical Considerations for Next-Generation Proteomics
    note: null
    pmcid: PMC8185883
    pmid: '33904308'
    type:
    - Primary
    version: null
  relation: []
  toolType: []
  topic: []
  validated: 0
  version: []
- accessibility: Open access
  additionDate: '2023-07-26T14:40:01.768324Z'
  biotoolsCURIE: biotools:ms_annika
  biotoolsID: ms_annika
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: viktoria.dorfer@fh-hagenberg.at
    fundrefid: null
    gridid: null
    name: Viktoria Dorfer
    note: null
    orcidid: https://orcid.org/0000-0002-5332-5701
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: http://bioinformatics.fh-hagenberg.at/
  - email: micha.birklbauer@fh-hagenberg.at
    fundrefid: null
    gridid: null
    name: Micha Birklbauer
    note: null
    orcidid: https://orcid.org/0009-0005-1051-179X
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    url: http://bioinformatics.fh-hagenberg.at/
  description: MS Annika is a crosslink search engine based on MS Amanda, aimed at
    identifying crosslinks of cleavable and non-cleavable crosslinkers from MS2 and
    MS3 spectra. It can deal with a wide variety of cross-linkers and provides robust
    and transparent FDR control based on a target-decoy approach. MS Annika is available
    free of charge as a plug-in for Proteome Discoverer.
  documentation:
  - note: null
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    note: null
    operation:
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      format:
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      format:
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    - data:
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      format:
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      - term: SVG
        uri: http://edamontology.org/format_3604
    - data:
        term: Score
        uri: http://edamontology.org/data_1772
      format:
      - term: TSV
        uri: http://edamontology.org/format_3475
  homepage: https://github.com/oschwengers/bakta
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2025-09-01T07:59:35.735958Z'
  license: GPL-3.0
  link:
  - note: null
    type:
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    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
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  name: Bakta
  operatingSystem:
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  otherID: []
  owner: oschwengers
  publication:
  - doi: 10.1099/mgen.0.000685
    metadata:
      abstract: ''
      authors: []
      citationCount: 582
      date: '2021-01-01T00:00:00Z'
      journal: Microbial Genomics
      title: 'Bakta: Rapid and standardized annotation of bacterial genomes via alignment-free
        sequence identification'
    note: null
    pmcid: PMC8743544
    pmid: '34739369'
    type:
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    version: '1.1'
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    type: uses
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    type: uses
  - biotoolsID: infernal
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  - biotoolsID: trnascan-se
    type: uses
  - biotoolsID: blast
    type: uses
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    type: uses
  - biotoolsID: pilercr
    type: uses
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    type: uses
  toolType:
  - Command-line tool
  - Web application
  topic:
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    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:
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- accessibility: Open access
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  biotoolsCURIE: biotools:macsylib
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    orcidid: null
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    typeEntity: Institute
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    url: null
  - email: null
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    gridid: null
    name: Microbial Evolutionary Genomics Unit
    note: null
    orcidid: null
    rorid: null
    typeEntity: Division
    typeRole: []
    url: https://research.pasteur.fr/en/team/microbial-evolutionary-genomics/
  - email: null
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    name: Bioinformatics and Biostatistics HUB
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    orcidid: null
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    typeEntity: Division
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    url: https://research.pasteur.fr/en/team/bioinformatics-and-biostatistics-hub/
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    name: Eduardo P.C. Rocha
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    name: Sophie Abby
    note: null
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    url: null
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    name: Bertrand Néron
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  description: a Python package library that allow to model and detect macromolecular
    systems, genetic pathways… by similarity search in prokaryotes datasets.
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    type:
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  download:
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    type: Source code
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    input:
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      format: []
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    note: null
    operation:
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  homepage_status: 0
  language:
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  lastUpdate: '2025-08-11T12:14:42.322020Z'
  license: GPL-3.0
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    type:
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    type:
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  otherID: []
  owner: bneron
  publication:
  - doi: 10.24072/pcjournal.250
    metadata:
      abstract: 'Complex cellular functions are usually encoded by a set of genes
        in one or a few orga-nized genetic loci in microbial genomes. Macromolecular
        System Finder (MacSyFinder) is a program that uses these properties to model
        and then annotate cellular functions in microbial genomes. This is done by
        integrating the identification of each individual gene at the level of the
        molecular system. We hereby present a major release of MacSyFinder (version
        2) coded in Python 3. The code was improved and rationalized to facilitate
        future maintainability. Several new features were added to allow more flexible
        modelling of the systems. We introduce a more intuitive and comprehensive
        search engine to identify all the best candidate systems and sub-optimal ones
        that respect the models’ constraints. We also introduce the novel macsydata
        companion tool that enables the easy installation and broad distribution of
        the models developed for MacSyFinder (macsy-models) from GitHub repositories.
        Finally, we have updated and improved MacSyFinder popular mod-els: TXSScan
        to identify protein secretion systems, TFFscan to identify type IV filaments,
        CONJscan to identify conjugative systems, and CasFinder to identify CRISPR
        associated proteins. MacSyFinder and the updated models are available at:
        https://github.com/gem-pasteur/macsyfinder.'
      authors:
      - name: Neron B.
      - name: Denise R.
      - name: Coluzzi C.
      - name: Touchon M.
      - name: Rocha E.P.C.
      - name: Abby S.S.
      citationCount: 43
      date: '2023-01-01T00:00:00Z'
      journal: Peer Community Journal
      title: 'MacSyFinder v2: Improved modelling and search engine to identify molecular
        systems in genomes'
    note: null
    pmcid: null
    pmid: null
    type: []
    version: null
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  toolType:
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  topic:
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    uri: http://edamontology.org/topic_0085
  validated: 0
  version:
  - 1.0.1
- accessibility: null
  additionDate: '2025-07-24T07:14:51.692628Z'
  biotoolsCURIE: biotools:eukcc
  biotoolsID: eukcc
  collectionID: []
  confidence_flag: null
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  description: EukCC is a completeness and contamination estimator for metagenomic
    assembled microbial eukaryotic genomes.
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  download: []
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  function:
  - cmd: null
    input:
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        term: DNA sequence
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      format: []
    - data:
        term: Protein sequence record
        uri: http://edamontology.org/data_2886
      format: []
    note: null
    operation:
    - term: Sequence assembly validation
      uri: http://edamontology.org/operation_3180
    output:
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      format: []
  homepage: https://github.com/EBI-Metagenomics/EukCC
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2025-07-24T07:14:51.694965Z'
  license: GPL-3.0
  link: []
  maturity: null
  name: EukCC
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  owner: m.bernt
  publication:
  - doi: 10.1186/s13059-020-02155-4
    metadata:
      abstract: Microbial eukaryotes constitute a significant fraction of biodiversity
        and have recently gained more attention, but the recovery of high-quality
        metagenomic assembled eukaryotic genomes is limited by the current availability
        of tools. To help address this, we have developed EukCC, a tool for estimating
        the quality of eukaryotic genomes based on the automated dynamic selection
        of single copy marker gene sets. We demonstrate that our method outperforms
        current genome quality estimators, particularly for estimating contamination,
        and have applied EukCC to datasets derived from two different environments
        to enable the identification of novel eukaryote genomes, including one from
        the human skin.
      authors:
      - name: Saary P.
      - name: Mitchell A.L.
      - name: Finn R.D.
      citationCount: 70
      date: '2020-09-10T00:00:00Z'
      journal: Genome Biology
      title: Estimating the quality of eukaryotic genomes recovered from metagenomic
        analysis with EukCC
    note: null
    pmcid: null
    pmid: null
    type: []
    version: null
  relation: []
  toolType:
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  topic:
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    uri: http://edamontology.org/topic_3174
  validated: 0
  version: []
- accessibility: Open access
  additionDate: '2025-07-14T08:21:28.942611Z'
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  biotoolsID: UniversalMer
  collectionID: []
  confidence_flag: tool
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  description: UniversalMer is a k-mer counting tool for multiple size of k at once.
    It is available for DNA, RNA, and protein sequences. The program counts and summarizes
    the exact frequency of all k-mers from 1-mer to a user-defined maximum length
    (kmax). Analyzing the k-mer spectrum across multiple values of k can be done in
    seconds. This program is designed for bioinformatics researchers and scientists.
  documentation: []
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  function:
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    input:
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    - data:
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      format:
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    - data:
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      format:
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        uri: http://edamontology.org/format_2546
    note: null
    operation:
    - term: k-mer counting
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    output:
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      format: []
    - data:
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    - data:
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  homepage_status: 0
  language:
  - C++
  - C
  lastUpdate: '2025-07-14T08:21:28.944946Z'
  license: Freeware
  link:
  - note: null
    type:
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    url: https://sourceforge.net/projects/universal-mer/
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  name: UniversalMer
  operatingSystem:
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  otherID: []
  owner: Ugrammer
  publication: []
  relation: []
  toolType:
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  topic:
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    uri: http://edamontology.org/topic_0091
  - term: Data mining
    uri: http://edamontology.org/topic_3473
  - term: Sequence analysis
    uri: http://edamontology.org/topic_0080
  validated: 0
  version:
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- accessibility: Open access
  additionDate: '2022-02-07T23:41:36.733362Z'
  biotoolsCURIE: biotools:proteinprompt
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    note: null
    orcidid: https://orcid.org/0000-0002-6719-2997
    rorid: null
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    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Peter W. Hildebrand
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  - email: null
    fundrefid: null
    gridid: null
    name: Sebastian Canzler
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    orcidid: https://orcid.org/0000-0001-7935-9582
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  - email: null
    fundrefid: null
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    name: Markus Fischer
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  - email: null
    fundrefid: null
    gridid: null
    name: David Ulbricht
    note: null
    orcidid: null
    rorid: null
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  - email: null
    fundrefid: null
    gridid: null
    name: Nikola Ristic
    note: null
    orcidid: null
    rorid: null
    typeEntity: null
    typeRole: []
    url: null
  description: A webserver for predicting protein-protein interactions.
  documentation: []
  download: []
  editPermission:
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  function:
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    input:
    - data:
        term: Protein sequence
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      format: []
    note: null
    operation:
    - term: Protein interaction prediction
      uri: http://edamontology.org/operation_2492
    - term: Database search
      uri: http://edamontology.org/operation_2421
    - term: Protein-protein binding site prediction
      uri: http://edamontology.org/operation_2464
    output: []
  homepage: http://proteinformatics.org/ProteinPrompt
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2025-07-02T08:39:17.251278Z'
  license: null
  link:
  - note: null
    type:
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  name: ProteinPrompt
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  otherID: []
  owner: Jennifer
  publication:
  - doi: 10.1101/2021.09.03.458859
    metadata: null
    note: null
    pmcid: null
    pmid: null
    type: []
    version: null
  relation: []
  toolType:
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  topic:
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    uri: http://edamontology.org/topic_0128
  - term: Machine learning
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  - term: Protein interaction experiment
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  - term: Proteomics
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- accessibility: Open access
  additionDate: '2018-05-28T14:50:09Z'
  biotoolsCURIE: biotools:deepsig
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  cost: Free of charge
  credit:
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    gridid: null
    name: ELIXIR-ITA-BOLOGNA
    note: null
    orcidid: null
    rorid: null
    typeEntity: Institute
    typeRole:
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    url: http://biocomp.unibo.it
  - email: castrense.savojardo2@unibo.it
    fundrefid: null
    gridid: null
    name: Castrense Savojardo
    note: null
    orcidid: https://orcid.org/0000-0002-7359-0633
    rorid: null
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    url: null
  - email: pierluigi.martelli@unibo.it
    fundrefid: null
    gridid: null
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    note: null
    orcidid: https://orcid.org/0000-0002-0274-5669
    rorid: null
    typeEntity: Person
    typeRole:
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    url: http://biocomp.unibo.it
  description: Prediction of secretory signal peptides in protein sequences
  documentation:
  - note: null
    type:
    - Command-line options
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  download:
  - note: null
    type: Source code
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    type: Container file
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  function:
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    input:
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        term: Protein sequence (raw)
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      format:
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        uri: http://edamontology.org/format_1929
    - data:
        term: Taxonomy
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    note: null
    operation:
    - term: Protein signal peptide detection
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    output:
    - data:
        term: Protein report
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      format:
      - term: HTML
        uri: http://edamontology.org/format_2331
  homepage: https://busca.biocomp.unibo.it/deepsig/
  homepage_status: 0
  language:
  - Python
  - C++
  lastUpdate: '2025-06-19T11:55:09.017105Z'
  license: GPL-3.0
  link: []
  maturity: Mature
  name: DeepSig
  operatingSystem:
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  - Mac
  otherID: []
  owner: ELIXIR-ITA-BOLOGNA
  publication:
  - doi: 10.1093/bioinformatics/btx818
    metadata:
      abstract: Motivation The identification of signal peptides in protein sequences
        is an important step toward protein localization and function characterization.
        Results Here, we present DeepSig, an improved approach for signal peptide
        detection and cleavage-site prediction based on deep learning methods. Comparative
        benchmarks performed on an updated independent dataset of proteins show that
        DeepSig is the current best performing method, scoring better than other available
        state-of-the-art approaches on both signal peptide detection and precise cleavage-site
        identification. Availability and implementation DeepSig is available as both
        standalone program and web server at https://deepsig.biocomp.unibo.it. All
        datasets used in this study can be obtained from the same website.
      authors:
      - name: Savojardo C.
      - name: Martelli P.L.
      - name: Fariselli P.
      - name: Casadio R.
      citationCount: 96
      date: '2018-05-15T00:00:00Z'
      journal: Bioinformatics
      title: 'DeepSig: Deep learning improves signal peptide detection in proteins'
    note: null
    pmcid: PMC5946842
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    type:
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    version: '1.0'
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    uri: http://edamontology.org/topic_3510
  - term: Protein properties
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- accessibility: null
  additionDate: '2016-06-24T11:36:59Z'
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  description: Project that aims to identify orthologs among publicly available, complete
    genomes. With many hundreds of genomes analyzed to date, it is one of the largest
    projects of its kind.
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  - note: null
    type:
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    url: https://omabrowser.org/oma/about/
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    input:
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      format: []
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      format: []
    - data:
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    note: orthology prediction and paralogy OMA group
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  owner: adrian.altenhoff
  publication:
  - doi: 10.1093/nar/gku1158
    metadata:
      abstract: 'The Orthologous Matrix (OMA) project is a method and associated database
        inferring evolutionary relationships amongst currently 1706 complete proteomes
        (i.e. the protein sequence associated for every protein-coding gene in all
        genomes). In this update article, we present six major new developments in
        OMA: (i) a new web interface; (ii) Gene Ontology function predictions as part
        of the OMA pipeline; (iii) better support for plant genomes and in particular
        homeologs in the wheat genome; (iv) a new synteny viewer providing the genomic
        context of orthologs; (v) statically computed hierarchical orthologous groups
        subsets downloadable in OrthoXML format; and (vi) possibility to export parts
        of the all-against-all computations and to combine them with custom data for
        ''client-side'' orthology prediction. OMA can be accessed through the OMA
        Browser and various programmatic interfaces at http://omabrowser.org.'
      authors:
      - name: Altenhoff A.M.
      - name: Sunca N.
      - name: Glover N.
      - name: Train C.-M.
      - name: Sueki A.
      - name: Pilizota I.
      - name: Gori K.
      - name: Tomiczek B.
      - name: Muller S.
      - name: Redestig H.
      - name: Gonnet G.H.
      - name: Dessimoz C.
      citationCount: 160
      date: '2015-01-28T00:00:00Z'
      journal: Nucleic Acids Research
      title: 'The OMA orthology database in 2015: Function predictions, better plant
        support, synteny view and other improvements'
    note: null
    pmcid: PMC4383958
    pmid: '25399418'
    type:
    - Primary
    version: null
  - doi: 10.1093/nar/gkad1020
    metadata:
      abstract: In this update paper, we present the latest de v elopments in the
        OMA browser knowledgebase, whichãims to provide high-quality orthology inferencesãnd
        facilitate the study of gene families, genomesãnd their evolution. First,
        we discuss theãddition of new species in the database, particularlyãn expanded
        representation of prokaryotic species. The OMA browser now offers Ancestral
        Genome pagesãndãn Ancestral Gene Order vie w er,ãllo wing users to e xplore
        the e v olutionar y histor yãnd gene content ofãncestral genomes. Weãlso introduceã
        re vãmped L ocal Synten y Vie w er to compare genomic neighborhoodsãcross
        both e xtantãndãncestral genomes. Hierarchical Orthologous Groups (H O Gs)ãre
        nowãnnotated with Gene Ontologyãnnotations,ãnd users can easily perform extant
        orãncestral GO enrichments. Finally, we recap new tools in the OMA Ecosystem,
        including OMAmer for proteome mapping, OMArk for proteome qualityãssessment,
        OMAMO for model organism selectionãnd Read2Tree for phylogenetic species tree
        construction from reads. These new features provide exciting opportunities
        for orthologyãnalysisãnd comparative genomics. OMA isãccessibleãt https://omabrowser.org
        .
      authors:
      - name: Altenhoff A.M.
      - name: Vesztrocy A.W.
      - name: Bernard C.
      - name: Train C.-M.
      - name: Nicheperovich A.
      - name: Banos S.P.
      - name: Julca I.
      - name: Moi D.
      - name: Nevers Y.
      - name: Majidian S.
      - name: Dessimoz C.
      - name: Glover N.M.
      citationCount: 24
      date: '2024-01-05T00:00:00Z'
      journal: Nucleic Acids Research
      title: 'OMA or tholog y in 2024: impro v ed prokary ot e co v erãg e,ãncestralãnd
        extant GO enrichment,ã revamped synteny viewerãnd more in the OMA Ecosystem'
    note: null
    pmcid: null
    pmid: null
    type:
    - Primary
    version: null
  - doi: 10.1093/nar/gkaa1007
    metadata:
      abstract: OMA is an established resource to elucidate evolutionary relationships
        among genes from currently 2326 genomes covering all domains of life. OMA
        provides pairwise and groupwise orthologs, functional annotations, local and
        global gene order conservation (synteny) information, among many other functions.
        This update paper describes the reorganisation of the database into gene-,
        group- and genome-centric pages. Other new and improved features are detailed,
        such as reporting of the evolutionarily best conserved isoforms of alternatively
        spliced genes, the inferred local order of ancestral genes, phylogenetic profiling,
        better cross-references, fast genome mapping, semantic data sharing via RDF,
        as well as a special coronavirus OMA with 119 viruses from the Nidovirales
        order, including SARS-CoV-2, the agent of the COVID-19 pandemic. We conclude
        with improvements to the documentation of the resource through primers, tutorials
        and short videos. OMA is accessible at https://omabrowser.org.
      authors:
      - name: Altenhoff A.M.
      - name: Train C.-M.
      - name: Gilbert K.J.
      - name: Mediratta I.
      - name: de Farias T.M.
      - name: Moi D.
      - name: Nevers Y.
      - name: Radoykova H.-S.
      - name: Rossier V.
      - name: Vesztrocy A.W.
      - name: Glover N.M.
      - name: Dessimoz C.
      citationCount: 135
      date: '2021-01-08T00:00:00Z'
      journal: Nucleic Acids Research
      title: 'OMA orthology in 2021: Website overhaul, conserved isoforms, ancestral
        gene order and more'
    note: null
    pmcid: null
    pmid: null
    type:
    - Primary
    version: null
  - doi: 10.1093/nar/gkx1019
    metadata:
      abstract: 'The Orthologous Matrix (OMA) is a leading resource to relate genes
        across many species from all of life. In this update paper, we review the
        recent algorithmic improvements in the OMA pipeline, describe increases in
        species coverage (particularly in plants and early-branching eukaryotes) and
        introduce several new features in the OMA web browser. Notable improvements
        include: (i) a scalable, interactive viewer for hierarchical orthologous groups;
        (ii) protein domain annotations and domain-based links between orthologous
        groups; (iii) functionality to retrieve phylogenetic marker genes for a subset
        of species of interest; (iv) a new synteny dot plot viewer; and (v) an overhaul
        of the programmatic access (REST API and semantic web), which will facilitate
        incorporation of OMA analyses in computational pipelines and integration with
        other bioinformatic resources. OMA can be freely accessed at https://omabrowser.org.'
      authors:
      - name: Altenhoff A.M.
      - name: Glover N.M.
      - name: Train C.-M.
      - name: Kaleb K.
      - name: Warwick Vesztrocy A.
      - name: Dylus D.
      - name: De Farias T.M.
      - name: Zile K.
      - name: Stevenson C.
      - name: Long J.
      - name: Redestig H.
      - name: Gonnet G.H.
      - name: Dessimoz C.
      citationCount: 168
      date: '2018-01-01T00:00:00Z'
      journal: Nucleic Acids Research
      title: 'The OMA orthology database in 2018: Retrieving evolutionary relationships
        among all domains of life through richer web and programmatic interfaces'
    note: null
    pmcid: null
    pmid: null
    type:
    - Primary
    version: null
  relation: []
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  topic:
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  - term: Comparative genomics
    uri: http://edamontology.org/topic_0797
  validated: 1
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    operation:
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  name: BioSurfDB
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  publication:
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    metadata:
      abstract: 'Crude oil extraction, transportation and use provoke the contamination
        of countless ecosystems. Therefore, bioremediation through surfactants mobilization
        or biodegradation is an important subject, both economically and environmentally.
        Bioremediation research had a great boost with the recent advances in Metagenomics,
        as it enabled the sequencing of uncultured microorganisms providing new insights
        on surfactant-producing and/or oil-degrading bacteria. Many research studies
        are making available genomic data from unknown organisms obtained from metagenomics
        analysis of oil-contaminated environmental samples. These new datasets are
        presently demanding the development of new tools and data repositories tailored
        for the biological analysis in a context of bioremediation data analysis.
        This work presents BioSurfDB, www.biosurfdb.org, a curated relational information
        system integrating data from: (i) metagenomes; (ii) organisms; (iii) biodegradation
        relevant genes; proteins and their metabolic pathways; (iv) bioremediation
        experiments results, with specific pollutants treatment efficiencies by surfactant
        producing organisms; and (v) a biosurfactant-curated list, grouped by producing
        organism, surfactant name, class and reference. The main goal of this repository
        is to gather information on the characterization of biological compounds and
        mechanisms involved in biosurfactant production and/or biodegradation and
        make it available in a curated way and associated with a number of computational
        tools to support studies of genomic and metagenomic data.'
      authors:
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      - name: Araujo W.
      - name: Sales A.I.L.
      - name: De Brito Guerra A.
      - name: Da Silva Araujo S.C.
      - name: De Vasconcelos A.T.R.
      - name: Agnez-Lima L.F.
      - name: Freitas A.T.
      citationCount: 30
      date: '2015-01-01T00:00:00Z'
      journal: Database
      title: 'BioSurfDB: Knowledge and algorithms to support biosurfactants and biodegradation
        studies'
    note: null
    pmcid: null
    pmid: null
    type:
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    version: null
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  - term: Enzymes
    uri: http://edamontology.org/topic_0821
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  version: []
- accessibility: Open access
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  description: PEP-FOLD4 is a fast and accurate structure prediction tool for peptides
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    url: null
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    url: null
  - email: null
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    note: null
    orcidid: https://orcid.org/0000-0003-1953-5606
    rorid: null
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    url: null
  description: shic is a collection of shims for use in automated workflow composition
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    note: null
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    note: null
    operation:
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    output:
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      format:
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    input:
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    note: null
    operation:
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    note: null
    operation:
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    output:
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    input:
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    note: null
    operation:
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      uri: http://edamontology.org/operation_3434
    output:
    - data:
        term: Protein name (UniProt)
        uri: http://edamontology.org/data_2764
      format:
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        uri: http://edamontology.org/format_2330
  homepage: https://github.com/magnuspalmblad/shic
  homepage_status: 0
  language: []
  lastUpdate: '2025-01-16T16:39:33.218764Z'
  license: MIT
  link:
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    type:
    - Repository
    url: https://github.com/magnuspalmblad/shic
  maturity: null
  name: shic
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- accessibility: Open access
  additionDate: '2024-05-05T10:53:14.688391Z'
  biotoolsCURIE: biotools:phiembed
  biotoolsID: phiembed
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: gonzales.markedward@gmail.com
    fundrefid: null
    gridid: null
    name: Mark Edward M. Gonzales
    note: Research Assistant, Bioinformatics Lab, Advanced Research Institute for
      Informatics, Computing and Networking, De La Salle University, Manila, Philippines
    orcidid: https://orcid.org/0000-0001-5050-3157
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    url: https://github.com/memgonzales
  - email: jennifer.ureta@gmail.com
    fundrefid: null
    gridid: null
    name: Jennifer C. Ureta
    note: Faculty, Bioinformatics Lab, Advanced Research Institute for Informatics,
      Computing and Networking, De La Salle University, Manila, Philippines
    orcidid: https://orcid.org/0000-0003-0427-5311
    rorid: null
    typeEntity: Person
    typeRole:
    - Contributor
    url: https://scholar.google.com/citations?user=v0Tf_u4AAAAJ&hl=en
  - email: anish.shrestha@dlsu.edu.ph
    fundrefid: null
    gridid: null
    name: Anish M.S. Shrestha
    note: Head, Bioinformatics Lab, Advanced Research Institute for Informatics, Computing
      and Networking, De La Salle University, Manila, Philippines
    orcidid: https://orcid.org/0000-0002-9192-9709
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: https://a-transposable-element.com/
  description: PHIEmbed is a phage-host interaction prediction tool that uses protein
    language models to represent the receptor-binding proteins of phages. It presents
    improvements over using handcrafted (manually feature-engineered) sequence properties
    and eliminates the need to manually extract and select features from phage sequences.
  documentation:
  - note: null
    type:
    - Installation instructions
    - Quick start guide
    - Citation instructions
    - Command-line options
    url: https://github.com/bioinfodlsu/phage-host-prediction
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  - note: null
    type: Source code
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    input:
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        term: Protein sequence
        uri: http://edamontology.org/data_2976
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
    note: Predicts the host genus of a phage given its receptor-binding protein sequences
    operation:
    - term: Prediction and recognition
      uri: http://edamontology.org/operation_2423
    output:
    - data:
        term: Report
        uri: http://edamontology.org/data_2048
      format:
      - term: CSV
        uri: http://edamontology.org/format_3752
  homepage: https://github.com/bioinfodlsu/phage-host-prediction
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2025-01-14T09:13:55.932761Z'
  license: MIT
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/bioinfodlsu/phage-host-prediction
  - note: null
    type:
    - Service
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  maturity: Emerging
  name: PHIEmbed
  operatingSystem:
  - Mac
  - Linux
  - Windows
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  publication:
  - doi: 10.1371/journal.pone.0289030
    metadata:
      abstract: With the growing interest in using phages to combat antimicrobial
        resistance, computational methods for predicting phage-host interactions have
        been explored to help shortlist candidate phages. Most existing models consider
        entire proteomes and rely on manual feature engineering, which poses difficulty
        in selecting the most informative sequence properties to serve as input to
        the model. In this paper, we framed phage-host interaction prediction as a
        multiclass classification problem that takes as input the embeddings of a
        phage’s receptor-binding proteins, which are known to be the key machinery
        for host recognition, and predicts the host genus. We explored different protein
        language models to automatically encode these protein sequences into dense
        embeddings without the need for additional alignment or structural information.
        We show that the use of embeddings of receptor-binding proteins presents improvements
        over handcrafted genomic and protein sequence features. The highest performance
        was obtained using the transformer-based protein language model ProtT5, resulting
        in a 3% to 4% increase in weighted F1 and recall scores across different prediction
        confidence thresholds, compared to using selected handcrafted sequence features.
      authors:
      - name: Gonzales M.E.M.
      - name: Ureta J.C.
      - name: Shrestha A.M.S.
      citationCount: 2
      date: '2023-07-01T00:00:00Z'
      journal: PLoS ONE
      title: Protein embeddings improve phage-host interaction prediction
    note: null
    pmcid: null
    pmid: '37486915'
    type:
    - Primary
    version: null
  relation: []
  toolType:
  - Command-line tool
  topic:
  - term: Machine learning
    uri: http://edamontology.org/topic_3474
  - term: Sequence analysis
    uri: http://edamontology.org/topic_0080
  - term: Proteins
    uri: http://edamontology.org/topic_0078
  - term: Proteomics
    uri: http://edamontology.org/topic_0121
  - term: Computational biology
    uri: http://edamontology.org/topic_3307
  - term: Bioinformatics
    uri: http://edamontology.org/topic_0091
  - term: Virology
    uri: http://edamontology.org/topic_0781
  validated: 0
  version: []
- accessibility: null
  additionDate: '2016-05-31T11:29:42Z'
  biotoolsCURIE: biotools:dynamine
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  credit:
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    fundrefid: null
    gridid: null
    name: vub.ac.be
    note: null
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    rorid: null
    typeEntity: Institute
    typeRole:
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    url: null
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    gridid: null
    name: Wim Vranken
    note: null
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    typeRole:
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    url: null
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    gridid: null
    name: Wim Vranken
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
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    - Primary contact
    url: null
  description: Protein backbone dynamics prediction from sequence.
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    type:
    - General
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      format:
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        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:
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        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: []
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  name: DynaMine
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  - Windows
  - Mac
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  owner: wvranken@vub.ac.be
  publication:
  - doi: 10.1038/ncomms3741
    metadata: null
    note: null
    pmcid: null
    pmid: '24225580'
    type:
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    version: null
  - doi: 10.1093/nar/gku270
    metadata: null
    note: null
    pmcid: PMC4086073
    pmid: '24728994'
    type:
    - Other
    version: null
  relation: []
  toolType:
  - Web API
  - Web application
  topic:
  - term: Biophysics
    uri: http://edamontology.org/topic_3306
  - term: Protein properties
    uri: http://edamontology.org/topic_0123
  - term: Protein disordered structure
    uri: http://edamontology.org/topic_3538
  validated: 1
  version:
  - '1'
- accessibility: null
  additionDate: '2020-11-09T21:38:53Z'
  biotoolsCURIE: biotools:trend_protein_evolution_function
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  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
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  download: []
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  elixir_badge: 0
  function:
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    input:
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        term: Protein sequence alignment
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      format:
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        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
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      - term: newick
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        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
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    - term: Phylogenetic inference
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      uri: http://edamontology.org/operation_0291
    - term: Sequence classification
      uri: http://edamontology.org/operation_2995
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    - 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
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      format:
      - term: newick
        uri: http://edamontology.org/format_1910
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      format:
      - term: JSON
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      - term: SVG
        uri: http://edamontology.org/format_3604
    - data:
        term: Sequence cluster (protein)
        uri: http://edamontology.org/data_1245
      format:
      - term: JSON
        uri: http://edamontology.org/format_3464
  homepage: http://trend.evobionet.com/
  homepage_status: 0
  language: []
  lastUpdate: '2024-12-17T20:42:49.942166Z'
  license: null
  link: []
  maturity: null
  name: TREND Protein Evolution Function
  operatingSystem: []
  otherID: []
  owner: vadim
  publication:
  - doi: 10.1093/nar/gkaa243
    metadata:
      abstract: Key steps in a computational study of protein function involve analysis
        of (i) relationships between homologous proteins, (ii) protein domain architecture
        and (iii) gene neighborhoods the corresponding proteins are encoded in. Each
        of these steps requires a separate computational task and sets of tools. Currently
        in order to relate protein features and gene neighborhoods information to
        phylogeny, researchers need to prepare all the necessary data and combine
        them by hand, which is time-consuming and error-prone. Here, we present a
        new platform, TREND (tree-based exploration of neighborhoods and domains),
        which can perform all the necessary steps in automated fashion and put the
        derived information into phylogenomic context, thus making evolutionary based
        protein function analysis more efficient. A rich set of adjustable components
        allows a user to run the computational steps specific to his task. TREND is
        freely available at http://trend.zhulinlab.org.
      authors:
      - name: Gumerov V.M.
      - name: Zhulin I.B.
      citationCount: 33
      date: '2021-01-01T00:00:00Z'
      journal: Nucleic Acids Research
      title: 'TREND: a platform for exploring protein function in prokaryotes based
        on phylogenetic, domain architecture and gene neighborhood analyses'
    note: null
    pmcid: PMC7319448
    pmid: '32282909'
    type:
    - Primary
    version: null
  - doi: 10.1093/nar/gkac034
    metadata:
      abstract: TheURL address of the web server published in this article has been
        changed fromhttp://trend.zhulinlab.org to http://trend. evobionet.com/.
      authors:
      - name: Gumerov V.M.
      - name: Zhulin I.B.
      citationCount: 6
      date: '2022-02-22T00:00:00Z'
      journal: Nucleic Acids Research
      title: 'Erratum: TREND: A platform for exploring protein function in prokaryotes
        based on phylogenetic, domain architecture and gene neighborhood analyses
        (Nucleic Acids Research DOI: 10.1093/nar/gkaa243)'
    note: 'Can be also accessed at this URL: https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkac034/6517937'
    pmcid: PMC8860576
    pmid: '35100406'
    type:
    - Other
    version: null
  relation: []
  toolType:
  - Web service
  topic:
  - term: Evolutionary biology
    uri: http://edamontology.org/topic_3299
  - term: Phylogeny
    uri: http://edamontology.org/topic_0084
  - term: Microbiology
    uri: http://edamontology.org/topic_3301
  - term: Protein sites, features and motifs
    uri: http://edamontology.org/topic_3510
  - term: Functional genomics
    uri: http://edamontology.org/topic_0085
  - term: Phylogenomics
    uri: http://edamontology.org/topic_0194
  - term: Bioinformatics
    uri: http://edamontology.org/topic_0091
  validated: 0
  version: []
- accessibility: null
  additionDate: '2015-12-06T15:18:34Z'
  biotoolsCURIE: biotools:svmhc
  biotoolsID: svmhc
  collectionID: []
  confidence_flag: null
  cost: null
  credit:
  - email: null
    fundrefid: null
    gridid: null
    name: bils.se
    note: null
    orcidid: null
    rorid: null
    typeEntity: Institute
    typeRole:
    - Provider
    url: null
  - email: arne@bioinfo.se
    fundrefid: null
    gridid: null
    name: null
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: null
  description: Prediction of MHC class I binding peptides.
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  download: []
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  elixir_badge: 0
  function:
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    input:
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    note: null
    operation:
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      uri: http://edamontology.org/operation_2423
    output:
    - data:
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  homepage: http://www.sbc.su.se/%7Epierre/svmhc/
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  description: Framework to predict localization in life's three domains, including
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    output:
    - data:
        term: Protein report
        uri: http://edamontology.org/data_0896
      format:
      - term: TSV
        uri: http://edamontology.org/format_3475
  homepage: https://rostlab.org/owiki/index.php/Loctree2
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  owner: a.merello@tum.de
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  - doi: 10.1093/bioinformatics/bts390
    metadata: null
    note: null
    pmcid: PMC3436817
    pmid: '22962467'
    type:
    - Primary
    version: null
  relation: []
  toolType:
  - Command-line tool
  topic:
  - term: Sequence analysis
    uri: http://edamontology.org/topic_0080
  - term: Protein properties
    uri: http://edamontology.org/topic_0123
  - term: Cell biology
    uri: http://edamontology.org/topic_2229
  validated: 1
  version:
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- accessibility: null
  additionDate: '2017-01-17T14:55:28Z'
  biotoolsCURIE: biotools:customprodb
  biotoolsID: customprodb
  collectionID:
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  cost: null
  credit:
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    fundrefid: null
    gridid: null
    name: xiaojing wang
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: null
  description: Generate customized protein sequence database from RNA-Seq data for
    proteomics search.
  documentation:
  - note: null
    type:
    - User manual
    url: http://bioconductor.org/packages/release/bioc/html/customProDB.html
  download:
  - note: null
    type: Source code
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    type: private
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  function:
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    input:
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        term: Annotation track
        uri: http://edamontology.org/data_3002
      format:
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        uri: http://edamontology.org/format_2572
      - term: Textual format
        uri: http://edamontology.org/format_2330
      - term: VCF
        uri: http://edamontology.org/format_3016
      - term: FASTA
        uri: http://edamontology.org/format_1929
    - data:
        term: Sequence alignment
        uri: http://edamontology.org/data_0863
      format:
      - term: BAM
        uri: http://edamontology.org/format_2572
      - term: Textual format
        uri: http://edamontology.org/format_2330
      - term: VCF
        uri: http://edamontology.org/format_3016
      - term: FASTA
        uri: http://edamontology.org/format_1929
    - data:
        term: Sequence variations
        uri: http://edamontology.org/data_3498
      format:
      - term: BAM
        uri: http://edamontology.org/format_2572
      - term: Textual format
        uri: http://edamontology.org/format_2330
      - term: VCF
        uri: http://edamontology.org/format_3016
      - term: FASTA
        uri: http://edamontology.org/format_1929
    - data:
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      - term: BAM
        uri: http://edamontology.org/format_2572
      - term: Textual format
        uri: http://edamontology.org/format_2330
      - term: VCF
        uri: http://edamontology.org/format_3016
      - term: FASTA
        uri: http://edamontology.org/format_1929
    - data:
        term: COSMIC ID
        uri: http://edamontology.org/data_3264
      format:
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        uri: http://edamontology.org/format_2572
      - term: Textual format
        uri: http://edamontology.org/format_2330
      - term: VCF
        uri: http://edamontology.org/format_3016
      - term: FASTA
        uri: http://edamontology.org/format_1929
    note: null
    operation:
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      uri: http://edamontology.org/operation_3429
    - term: Sequence annotation
      uri: http://edamontology.org/operation_0361
    output:
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        term: Protein sequence record
        uri: http://edamontology.org/data_2886
      format:
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  homepage: http://bioconductor.org/packages/release/bioc/html/customProDB.html
  homepage_status: 0
  language:
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  lastUpdate: '2024-11-25T15:27:36.331211Z'
  license: Artistic-2.0
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  operatingSystem:
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  - Windows
  - Mac
  otherID: []
  owner: bioconductor_import
  publication:
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    metadata: null
    note: null
    pmcid: PMC3842753
    pmid: '24058055'
    type:
    - Primary
    version: null
  relation: []
  toolType:
  - Command-line tool
  - Library
  topic:
  - term: Data integration and warehousing
    uri: http://edamontology.org/topic_3366
  - term: RNA-Seq
    uri: http://edamontology.org/topic_3170
  - term: Sequencing
    uri: http://edamontology.org/topic_3168
  validated: 1
  version:
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next: ?page=2
previous: null
