PSORTb protocols

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PSORTb specifications

Information


Unique identifier OMICS_03892
Name PSORTb
Alternative name PSORT-B
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes
Wikipedia https://en.wikipedia.org/wiki/PSORTdb

Maintainer


  • person_outline PSORTb <>

Additional information


http://www.psort.org/documentation/index.html

Information


Unique identifier OMICS_03892
Name PSORTb
Alternative name PSORT-B
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS
Programming languages Perl
Computer skills Advanced
Version 3.0.5
Stability Stable
Requirements
BioPerl, NCBI BLAST, PFTOOLS
Maintained Yes

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Maintainer


  • person_outline PSORTb <>

Additional information


http://www.psort.org/documentation/index.html

Publications for PSORTb

PSORTb in pipelines

 (49)
2018
PMCID: 5804310
PMID: 29412357
DOI: 10.1590/0074-02760170340

[…] individual ion scores greater than 30 were considered. scaffold and the blast2go (https://www.blast2go.com/b2ghome) were used for functional annotation and analysis with the proteins identified. psortb v. 3.0 was used to predict the subcellular localisation (www.psort.org/psortb/) and signalp to predict the presence and location of signal peptide cleavage. kalign software in the clustal 2.1 […]

2018
PMCID: 5836817
PMID: 29504898
DOI: 10.1186/s12864-018-4472-9

[…] analysis was made with help of conserved domains search services: kegg [], kegg oc [], cogs []; protein subcellular localization prediction software: tmhmm server v.2.0 [], signalp 4.1 server [], psortb version 3.0.2 [], interpro server [, ]. prophage sequences were revealed with help of phast (phage search tool) [, ]. wgs data are available in genbank: accession numbers are cp017433 (a. […]

2017
PMCID: 5206647
PMID: 28045121
DOI: 10.1038/srep39824

[…] variable modification, ms tolerance of 100 ppm, ms/ms tolerance of 0.6 da. known contaminant ions (keratin) were excluded. the subcellular locations of the proteins were determined using the program psortb version 2.0 (http://www.psort.org/psortb/). protein bands from the repeated experiments were used for ms analysis and the same results were obtained., standard pcr and molecular biology […]

2017
PMCID: 5209532
PMID: 28066819
DOI: 10.1128/mSystems.00141-16

[…] acid sequences encoded by all predicted genes in each genome. amino acid sequences of the identified proteins were also submitted to the bacterial protein subcellular localization prediction tool (psortb 3.0) () to identify signal peptides linked to specific cellular compartments. furthermore, genomes were submitted to antismash 3.0 () for the prediction of a putative biosynthetic gene cluster […]

2017
PMCID: 5300222
PMID: 28182704
DOI: 10.1371/journal.pone.0171944

[…] protection [, , ]., the functionality and domain classification of 14 proteins () was conducted by interpro []. the subcellular localization of the individual proteins was predicted by the cello and psortb predictor [, ] that provide an output with reliability score for each location of each protein. commonly, protective b-cell protein antigens are located in the outer membrane and extracellular […]


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PSORTb in publications

 (452)
PMCID: 5954444
PMID: 29780242
DOI: 10.1177/1177932218755337

[…] it is possible to select sequence options with or without transmembrane sets. all analyses were conducted with gram-positive bacteria using 2 neural networks. a second subcellular location software, psortb 3.0.2 (available at http://www.expasy.org/proteomics) was used consisting in multiple analytical modules, each one analyzing a biologic resource known for influencing or being typical […]

PMCID: 5948995
PMID: 29686091
DOI: 10.1073/pnas.1800650115

[…] cifa-like homologs (), whereas cifb has nuclease and deubiquitilase domains (, ). only the deubiquitilase annotation has been functionally tested and confirmed (). based on subcellular localization (psortb) and transmembrane helix predictors (tmbase), cifa is a cytoplasmic protein without transmembrane helices (fig. s3). codon-based and fisher’s exact tests of neutrality demonstrate that closely […]

PMCID: 5947290
PMID: 29468803
DOI: 10.1111/1462-2920.14077

[…] one cxxch motif and also matched a protein domain related to cytochrome c (see supporting information table s8). the subcellular localization of potential c‐type cytochromes was predicted using psortb (yu et al., ). based on their predicted localization, cytochromes were assigned to the following categories: cytoplasmic or periplasmic (c/p), membrane‐ or cell wall‐associated (m/w), […]

PMCID: 5895597
PMID: 29643357
DOI: 10.1038/s41467-018-03847-z

[…] was performed with a database containing protein sequences of the s. aureus usa300 fpr3757 genome downloaded from ncbiprot. the subcellular localization of each identified protein was predicted by psortb v.3.0 (www.psort.org/psorb/)., s. aureus strains were cultivated in 5 ml tsb at 37 °c to an od650 nm of 0.9. after centrifugation at 4 °c, the bacterial cells were mixed with glass beads […]

PMCID: 5877877
PMID: 29601598
DOI: 10.1371/journal.ppat.1006945

[…] proteins identified by mass spectrometric analysis were annotated for subcellular localization using four different available online bacterial protein subcellular localization (scl) predictor tools, psortb version 3.0.2 [], subloc v1.0 [], cello 2.5 [] and pslpred []. the predicted subcellular component was assigned based on majority votes. the identified protein was annotated as unknown […]


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PSORTb institution(s)
Department of Molecular Biology and Biochemistry, Burnaby, BC, Canada; School of Computing Science, Simon Fraser University, Burnaby, BC, Canada; Centre for High-Throughput Biology and Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, Canada
PSORTb funding source(s)
Supported by Natural Sciences and Engineering Research Council of Canada, with the support of the Cystic Fibrosis Foundation and Simon Fraser University Community Trust; BC Proteomics Network; Postgraduate Scholarship from the Natural Sciences and Engineering Research Council of Canada; Canadian Institutes of Health Research and Michael Smith Foundation for Health Research Strategic Training Program in Bioinformatics Graduate Award.

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