SignalP protocols

SignalP specifications

Information


Unique identifier OMICS_03894
Name SignalP
Alternative name SignalP-NN
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Documentation


Maintainer


  • person_outline Henrik Nielsen <>

Additional information


Access available upon request.

Information


Unique identifier OMICS_03894
Name SignalP
Alternative name SignalP-NN
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use Academic or non-commercial use
Input data A single amino acid sequence or several sequences.
Input format FASTA
Operating system Unix/Linux, Mac OS, Windows
Programming languages Perl
Computer skills Advanced
Version 4.1
Stability Stable
Requirements CYGWIN or MobaXterm (Windows only), GNUPLOT

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Documentation


Maintainer


This tool is not maintained anymore.

Additional information


Access available upon request.

Publications for SignalP

SignalP IN pipelines

 (278)
2018
PMCID: 5796565
PMID: 29435100
DOI: 10.1186/s40793-017-0306-7

[…] prokaryotic genome annotation pipeline [30] was used for automated genome annotation, and functional annotations were carried out by searching against kegg [31], cog [32] and pfam [33] databases. signalp [34] and tmhmm [35] tools were used for the prediction of genes with signal peptides and transmembrane helices, respectively. searches against ncbi-nr [36], refseq [37], uniprotkb/swiss-prot […]

2018
PMCID: 5800701
PMID: 29408937
DOI: 10.1371/journal.pone.0192433

[…] described in the literature: binding protein 1 –bip1 [35]; arylsulfatase 1 –ars1 [8], carbonic anhydrase 1 –cah1 [25], and ice-binding protein 1 –ibp1 [36], and six in silico identified sequences. signalp4.0 was used to predict sp sequences from a c. reinhardtii protein sequence dataset [37], as described in s6 fig. the assembly v4.0, dataset chlre4_best_protein.fasta, from the doe joint […]

2018
PMCID: 5800701
PMID: 29408937
DOI: 10.1371/journal.pone.0192433

[…] dataset [37], as described in s6 fig. the assembly v4.0, dataset chlre4_best_protein.fasta, from the doe joint genome institute databank was used [38]. the protein sequences dataset submitted to the signalp4.0, generated a dataset of 8556 possible sps. the in silico identified sps were submitted to a multiple sequence alignment by clustalw in mega7 [60] and used to generate a phylogenetic tree […]

2018
PMCID: 5811872
PMID: 29390140
DOI: 10.1093/gbe/evy023

[…] number of parameters. both methods “free” and “join” were compared in order to scan for positive selection. finally, putative secreted effector proteins were identified by predicting secretion using signalp 4.0 (petersen et al. 2011) and proteins were considered as secreted if the program indicated the presence of a signal peptide but no transmembrane domain., to detect residues under positive […]

2018
PMCID: 5851621
PMID: 29538430
DOI: 10.1371/journal.pone.0194088

[…] of 90 missing genes, i.e. undercalled pegs in the remaining gaps between features. genome properties and statistics are summarized in table 2. genes with signal peptides were detected with the signalp 4.1 server [85], and the crispr repeats, with the crispr reconigtion tool v1.0 [86]. details of clusters of orthologs groups are shown in s5 table., a detected with pfam v.31.0 […]

SignalP institution(s)
Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark; Novo Nordisk Foundation Center for Protein Research, Health Sciences Faculty, University of Copenhagen, Copenhagen, Denmark; Center for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden; Science for Life Laboratory, Stockholm University, Solna, Sweden

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