SignalP protocols

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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

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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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Publications for SignalP

SignalP in pipelines

 (844)
2018
PMCID: 5753508
PMID: 29298673
DOI: 10.1186/s12864-017-4407-x

[…] using wolf psort v0.2 software []. the resulting putative extracellular group of proteins was further screened for the presence of signal peptides and signal peptide cleavage sites using the signalp v4.0 program []. subsequently, all proteins with signal peptides were analyzed for the presence of transmembrane domains using phobius [] and tmhmm version 2.0 []. the set of proteins […]

2018
PMCID: 5765558
PMID: 29319806
DOI: 10.1093/gbe/evx271

[…] to classify the genes and to predict domains and sites. at runtime, the following databases were selected: tigrfam, prodom, smart, prosite, pfama, prints, superfamily, coils, and gene3d. priam (), signalp 4.0 (), and tmhmm () were used to assign enzyme commission numbers (ecs), to detect signal peptides, and to detect transmembrane protein topology, respectively. predictions and provenance […]

2018
PMCID: 5767910
PMID: 29349107
DOI: 10.1016/j.dib.2017.12.060

[…] for functional annotation, blast search results were analyzed with blast2go version 4.1 . cazymes were identified with dbcan version 5.0 . proteins predicted to contain a signal peptide by both signalp version 4.1 and targetp version 1.1 were categorized as secreted proteins. proteases were identified by homology (blast) searches against the merops database version 11.0 with a maximum […]

2018
PMCID: 5773612
PMID: 29348442
DOI: 10.1038/s41598-018-19219-y

[…] the theoretical molecular weight (mw) and isoelectric point (ip) of the nlncdase were predicted by using expasy server (http://www.expasy.org/tools/protparam.html). signal peptide was predicted by signalp 4.1 server (http://www.cbs.dtu.dk/services/signalp). the predicted amino acid sequence of the nlncdase gene was used as a query sequence to search sequences in national center […]

2018
PMCID: 5776133
PMID: 29387078
DOI: 10.3389/fpls.2017.02272

[…] center for biotechnology information (http://www.ncbi.nlm.nih.gov). phylogenetic analysis was performed using mega6 software (tamura et al., ). the putative motif and domains were analyzed with signalp 4.1 (http://www.cbs.dtu.dk/services/signalp/), interproscan (http://www.ebi.ac.uk/interpro/scan.html), and smart (http://smart.embl-heidelberg.de/). the sequences of the ssr markers […]


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SignalP in publications

 (3861)
PMCID: 5955625
PMID: 29774236
DOI: 10.1126/sciadv.aar4536

[…] membrane. as a follow-up to these observations, we used bioinformatics to determine whether the protein had a predicted signal peptide or a chloroplast targeting sequence. the combined algorithms of signalp v.3.0 (using neural networks) and asafind suggest that isip1 has a predicted n-terminal signal peptide but that it is not targeted to the chloroplast because it lacks the fwyl residue at +1 […]

PMCID: 5955954
PMID: 29769555
DOI: 10.1038/s41598-018-25654-8

[…] to a wild type sequence to identify insertions or deletions., the possible presence and location of a signal peptide in the blg variant encoded by lgb deletion alleles was determined using the signalp 4.1 server., two of the samples, 1601 and 1602, were sequenced using whole genome shotgun sequencing, producing 931,498,618 and 959,133,690 raw reads respectively. the raw reads […]

PMCID: 5954228
PMID: 29764946
DOI: 10.1128/mBio.00636-18

[…] length (). cegma v2.4.010312 was used to identify the presence of core eukaryotic-protein-coding genes and for subsequent evaluation of genome coverage (). secreted proteins were predicted using signalp v4.1 (no truncation to the sequence length) (), and transmembrane helices were predicted using tmhmm v2.0 (). potential pathogenic proteins were identified using blastp against pathogen-host […]

PMCID: 5954444
PMID: 29780242
DOI: 10.1177/1177932218755337

[…] of hydropathicity (gravy) were estimated by the protparam server (available at http://web.expasy.org/protparam)., to verify the peptide signal and consequently locate the c pseudotuberculosis, the signalp 4.1 software was used (available at http://www.expasy.org/proteomics). this tool contains 2 neural networks, where it is possible to select sequence options with or without transmembrane […]

PMCID: 5946483
PMID: 29747580
DOI: 10.1186/s12864-018-4739-1

[…] e value <1e-5 and identity > 40% against the transporter protein database, downloaded from transporter classification database []. the secretomes of 14 fungi in this study were identified by signalp 4.1 and tmhmm 2.0 []. core secondary metabolite (sm) genes and clusters were initially identified using antismash. cyps genes were identified with hmmer and then named using the cytochrome […]


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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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