PSORTb specifications

Information


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

Taxon


  • Eubacteria

Maintainer


  • person_outline PSORTb <>

Additional information


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

Information


Unique identifier OMICS_03892
Name PSORTb
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

Taxon


  • Eubacteria

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Maintainer


  • person_outline PSORTb <>

Additional information


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

PSORTb articles

PSORTb citations

 (3)
2011
PMCID: 3125140

[…] data [78], [79]. a total of 435 csaes that had more than two transmembrane domains were screened using the tmhmm algorithm [36], and the localization of the predicted proteins was determined using psortb based on homology to proteins of known localization [35]. csaes homologous to proteins of the free-living flatworm s. mediterranea, or of humans were selected using a cut-off e-value≤1e−10 […]

2007
PMCID: 1832192

[…] using the metacyc metabolic pathway database [41]. homologies were assessed using blast tools [86] hosted on the ncbi and tigr servers. additional subcellular localization was determined with psortb [60]. protein sequence alignments were performed using the clustalw multiple sequence alignment algorithm [87]., microarray results were verified by real-time quantitative rt-pcr (qrt-pcr), […]

2005
PMCID: 1314894

[…] all localizations in concert, preferably using a combination of both methods, to gain a more accurate view of a given protein's localization in the cell., when computational scl predictions by psortb v.2.0 were compared to the selected subproteomic studies from gram-negative bacteria (listed in table 1), 405 proteins were identified which met our selection criteria – the results […]

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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