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  description: DigestedProteinDB provides a scalable computational infrastructure
    for indexing and querying peptide cleavage data. Designed for seamless integration
    into high-throughput mass spectrometry pipelines, it enables low-latency searches
    and advanced filtering of digested protein datasets to accelerate experimental
    spectra cross-referencing.
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  homepage: https://digestedproteindb.pbf.hr
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  license: null
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  name: DigestedProteinDB
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  owner: janko
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  toolType:
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  topic:
  - term: Proteomics
    uri: http://edamontology.org/topic_0121
  validated: 0
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- accessibility: null
  additionDate: '2017-03-25T16:30:10Z'
  biotoolsCURIE: biotools:vigor
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    typeEntity: Person
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    - Primary contact
    url: null
  description: Gene prediction program for small viral genomes in support of high
    throughput feature prediction and annotation. Identified genome-specific features
    include frame shifts, ribosomal slippage, RNA editing, stop codon read-through,
    overlapping genes, embedded genes, and mature peptide cleavage sites.
  documentation:
  - note: null
    type:
    - General
    url: http://www.jcvi.org/vigor/howto.php
  download: []
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  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Homology-based gene prediction
      uri: http://edamontology.org/operation_3663
    - term: Gene prediction
      uri: http://edamontology.org/operation_2454
    - term: Coding region prediction
      uri: http://edamontology.org/operation_0436
    - term: Protein feature detection
      uri: http://edamontology.org/operation_3092
    output: []
  homepage: http://www.jcvi.org/vigor
  homepage_status: 0
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  lastUpdate: '2024-11-25T14:56:39.008022Z'
  license: null
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  name: VIGOR
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  owner: ELIXIR-EE
  publication:
  - doi: 10.1093/nar/gks528
    metadata: null
    note: null
    pmcid: PMC3394299
    pmid: '22669909'
    type: []
    version: null
  relation: []
  toolType:
  - Web application
  topic:
  - term: Virology
    uri: http://edamontology.org/topic_0781
  - term: Gene transcripts
    uri: http://edamontology.org/topic_3512
  - term: Gene structure
    uri: http://edamontology.org/topic_0114
  - term: Gene expression
    uri: http://edamontology.org/topic_0203
  validated: 1
  version: []
- accessibility: null
  additionDate: '2015-12-17T14:23:00Z'
  biotoolsCURIE: biotools:signalp
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  collectionID:
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  confidence_flag: null
  cost: Free of charge (with restrictions)
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  - email: null
    fundrefid: null
    gridid: null
    name: TN Petersen
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    typeRole:
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    typeEntity: Institute
    typeRole:
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    url: null
  - email: hnielsen@cbs.dtu.dk
    fundrefid: null
    gridid: null
    name: Henrik Nielsen
    note: null
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    rorid: null
    typeEntity: null
    typeRole:
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    url: null
  - email: hnielsen@cbs.dtu.dk
    fundrefid: null
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    typeEntity: Person
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    url: null
  description: Prediction of the presence and location of signal peptide cleavage
    sites in amino acid sequences from different organisms.
  documentation:
  - note: null
    type:
    - General
    url: http://www.cbs.dtu.dk/services/SignalP
  download:
  - note: null
    type: Source code
    url: http://www.cbs.dtu.dk/cgi-bin/sw_request?signalp
    version: null
  - note: null
    type: Binaries
    url: http://www.cbs.dtu.dk/cgi-bin/sw_request?signalp
    version: null
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  function:
  - cmd: null
    input:
    - data:
        term: Sequence
        uri: http://edamontology.org/data_2044
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
    note: predicts the presence and location of signal peptide cleavage sites in amino
      acid sequences from different organisms
    operation:
    - term: Protein signal peptide detection
      uri: http://edamontology.org/operation_0418
    - term: Protein cleavage site prediction
      uri: http://edamontology.org/operation_0422
    output:
    - data:
        term: Protein features
        uri: http://edamontology.org/data_1277
      format:
      - term: GFF
        uri: http://edamontology.org/format_2305
    - data:
        term: Sequence report
        uri: http://edamontology.org/data_2955
      format: []
  homepage: http://cbs.dtu.dk/services/SignalP/
  homepage_status: 0
  language: []
  lastUpdate: '2024-11-24T14:37:27.222979Z'
  license: Other
  link:
  - note: null
    type:
    - Repository
    url: http://www.cbs.dtu.dk/cgi-bin/sw_request?signalp
  maturity: Mature
  name: SignalP
  operatingSystem:
  - Linux
  - Mac
  otherID:
  - type: rrid
    value: rrid:SCR_015644
    version: null
  owner: lidiamorrone
  publication:
  - doi: 10.1038/nmeth.1701
    metadata:
      abstract: ''
      authors:
      - name: Petersen T.N.
      - name: Brunak S.
      - name: Von Heijne G.
      - name: Nielsen H.
      citationCount: 7535
      date: '2011-10-01T00:00:00Z'
      journal: Nature Methods
      title: 'SignalP 4.0: Discriminating signal peptides from transmembrane regions'
    note: null
    pmcid: null
    pmid: '21959131'
    type:
    - Primary
    version: null
  relation: []
  toolType:
  - Command-line tool
  - Web application
  topic:
  - term: Protein sites, features and motifs
    uri: http://edamontology.org/topic_3510
  validated: 1
  version:
  - '4.1'
- accessibility: null
  additionDate: '2015-01-21T13:29:25Z'
  biotoolsCURIE: biotools:tatp
  biotoolsID: tatp
  collectionID: []
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  cost: Free of charge (with restrictions)
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  - email: null
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    note: null
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  - email: hnielsen@cbs.dtu.dk
    fundrefid: null
    gridid: null
    name: Henrik Nielsen
    note: null
    orcidid: http://orcid.org/0000-0002-9412-9643
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: null
  description: Prediction of the presence and location of Twin-arginine signal peptide
    cleavage sites in bacteria.
  documentation:
  - note: null
    type:
    - General
    url: http://www.cbs.dtu.dk/services/TatP/instructions.php
  download: []
  editPermission:
    authors: []
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  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Sequence
        uri: http://edamontology.org/data_2044
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
    note: predicts the presence and location of Twin-arginine signal peptide cleavage
      sites in bacteria. Signal peptide/non-signal peptide prediction based on a combination
      of two artificial neural networks
    operation:
    - term: Protein signal peptide detection
      uri: http://edamontology.org/operation_0418
    - term: Protein cleavage site prediction
      uri: http://edamontology.org/operation_0422
    output:
    - 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/TatP/
  homepage_status: 0
  language: []
  lastUpdate: '2018-12-16T14:15:31Z'
  license: Other
  link:
  - note: null
    type:
    - Software catalogue
    url: http://cbs.dtu.dk/services
  maturity: Emerging
  name: TatP
  operatingSystem:
  - Linux
  otherID: []
  owner: CBS
  publication:
  - doi: 10.1186/1471-2105-6-167
    metadata:
      abstract: 'Background: Proteins carrying twin-arginine (Tat) signal peptides
        are exported into the periplasmic compartment or extracellular environment
        independently of the classical Sec-dependent translocation pathway. To complement
        other methods for classical signal peptide prediction we here present a publicly
        available method, TatP, for prediction of bacterial Tat signal peptides. Results:
        We have retrieved sequence data for Tat substrates in order to train a computational
        method for discrimination of Sec and Tat signal peptides. The TatP method
        is able to positively classify 91% of 35 known Tat signal peptides and 84%
        of the annotated cleavage sites of these Tat signal peptides were correctly
        predicted. This method generates far less false positive predictions on various
        datasets than using simple pattern matching. Moreover, on the same datasets
        TatP generates less false positive predictions than a complementary rule based
        prediction method. Conclusion: The method developed here is able to discriminate
        Tat signal peptides from cytoplasmic proteins carrying a similar motif, as
        well as from Sec signal peptides, with high accuracy. The method allows filtering
        of input sequences based on Perl syntax regular expressions, whereas hydrophobicity
        discrimination of Tat- and Sec-signal peptides is carried out by an artificial
        neural network. A potential cleavage site of the predicted Tat signal peptide
        is also reported. The TatP prediction server is available as a public web
        server at http://www.cbs.dtu.dk/ services/TatP/. © 2005 Bendtsen et al; licensee
        BioMed Central Ltd.'
      authors:
      - name: Bendtsen J.D.
      - name: Nielsen H.
      - name: Widdick D.
      - name: Palmer T.
      - name: Brunak S.
      citationCount: 377
      date: '2005-07-02T00:00:00Z'
      journal: BMC Bioinformatics
      title: Prediction of twin-arginine signal peptides
    note: null
    pmcid: PMC1182353
    pmid: '15992409'
    type:
    - Primary
    version: null
  relation: []
  toolType:
  - Web application
  - Web service
  topic:
  - term: Sequence sites, features and motifs
    uri: http://edamontology.org/topic_0160
  validated: 1
  version:
  - '1.0'
next: null
previous: null
