PSORTb protocols

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

 (9)
2017
PMCID: 5481527
PMID: 28585301
DOI: 10.1111/1751-7915.12731

[…] pstream of any of genes encoding the major omps of n. helminthoeca including p51, ssa or nsps (table 4)., a. location of outer member proteins is predicted by the psort‐b algorithm (http://psort.org/psortb). other putative omps (p51, nsp1/2/3 and ssa) are determined by homology searches to n. risticii and n. sennetsu protein database using blastp., the present study identified several other n. he […]

2016
PMCID: 4772473
PMID: 26928424
DOI: 10.1038/srep22438

[…] poorly characterized: (r: general function prediction only; s: function unknown)., abased on r. anatipestifer yb2 genome (accession number: cp007204)., bsubcellular locations were predicted by the psortb version 3.0 server (http://www.psort.org/)., cfunctional characterization of the proteins was predicted by searching against eggnog (version 3) database using blastp., dno related cog., […]

2015
PMCID: 4671577
PMID: 26642207
DOI: 10.1371/journal.pone.0144379

[…] sequence of cloned genes using pair wise alignment (http://www.ebi.ac.uk/tools/msa/clustalw2/). the sub-cellular location of cloned gene product was assessed in silico using signalp 4.0 [13] and psortb 3.1 [14]. in addition, homology based detection of cota sequence was carried out using ncbi-blastp tool against swissprot database. results of in silico analysis were compared […]

2014
PMCID: 4125193
PMID: 25101643
DOI: 10.1371/journal.pone.0104260

[…] for function prediction and reverse position specific (rps) blasts [32]. potential subcellular localization of identified cazymes was predicted by uploading fasta aa sequences of genes into the psortb 3.0 database [33] and using the final predictions., cell growth on 2 g/l xylan was quantified by measuring optical densities (od600) and protein concentration, as quantified using the modified […]

2014
PMCID: 4207797
PMID: 25340474
DOI: 10.1371/journal.pone.0110872

[…] of differentially expressed genes were analyzed for putative functions using ncbi protein blast and pfam 26.0 (http://pfam.janelia.org). subcellular localization of proteins was predicted using psortb version 3.0 (http://www.psort.org/)., semiquantitative reverse transcription (rt)-pcr was performed using superscript ii reverse transcriptase as outlined by the manufacturer (invitrogen). s. […]

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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