count: 3 list: - accessibility: null additionDate: '2015-12-17T14:23:00Z' biotoolsCURIE: biotools:signalp biotoolsID: signalp collectionID: - CBS community: null confidence_flag: null cost: Free of charge (with restrictions) credit: - email: null fundrefid: null gridid: null name: TN Petersen note: null orcidid: null rorid: null typeEntity: Person typeRole: - Developer url: null - email: null fundrefid: null gridid: null name: CBS note: null orcidid: null rorid: null typeEntity: Institute typeRole: - Provider url: null - 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: null typeRole: - Developer url: null - 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 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 editPermission: authors: - CBS 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: 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: '2019-11-11T14:45:04Z' 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: cbs_admin publication: - doi: 10.1038/nmeth.1701 metadata: abstract: '' authors: - name: Petersen T.N. - name: Brunak S. - name: Von Heijne G. - name: Nielsen H. citationCount: 6571 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: [] community: null 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: 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: [] type: private 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: 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' - accessibility: null additionDate: '2017-03-25T16:30:10Z' biotoolsCURIE: biotools:vigor biotoolsID: vigor collectionID: [] community: null confidence_flag: null cost: null credit: - email: shiliang@jcvi.org fundrefid: null gridid: null name: Support note: null orcidid: null rorid: null typeEntity: Person typeRole: - 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: [] editPermission: authors: [] type: private elixirCommunity: [] elixirNode: [] elixirPlatform: [] elixir_badge: 0 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: 1 language: [] lastUpdate: '2018-12-10T12:58:57Z' license: null link: [] maturity: null name: VIGOR operatingSystem: - Windows otherID: [] owner: ELIXIR-EE publication: - doi: null metadata: abstract: 'A gene prediction program, VIGOR (Viral Genome ORF Reader), was developed at J. Craig Venter Institute in 2010 and has been successfully performing gene calling in coronavirus, influenza, rhinovirus and rotavirus for projects at the Genome Sequencing Center for Infectious Diseases. VIGOR uses sequence similarity search against custom protein databases to identify protein coding regions, start and stop codons and other gene features. Ribonucleicacid editing and other features are accurately identified based on sequence similarity and signature residues. VIGOR produces four output files: a gene prediction file, a complementary DNA file, an alignment file, and a gene feature table file. The gene feature table can be used to create GenBank submission. VIGOR takes a single input: viral genomic sequences in FASTA format. VIGOR has been extended to predict genes for 12 viruses: measles virus, mumps virus, rubella virus, respiratory syncytial virus, alphavirus and Venezuelan equine encephalitis virus, norovirus, metapneumovirus, yellow fever virus, Japanese encephalitis virus, parainfluenza virus and Sendai virus. VIGOR accurately detects the complex gene features like ribonucleicacid editing, stop codon leakage and ribosomal shunting. Precisely identifying the mat-peptide cleavage for some viruses is a built-in feature of VIGOR. The gene predictions for these viruses have been evaluated by testing from 27 to 240 genomes from GenBank. © 2012 The Author(s).' authors: - name: Wang S. - name: Sundaram J.P. - name: Stockwell T.B. citationCount: 28 date: '2012-07-01T00:00:00Z' journal: Nucleic Acids Research title: VIGOR extended to annotate genomes for additional 12 different viruses note: null pmcid: null 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: [] next: null previous: null