PSAT pipeline

PSAT specifications

Information


Unique identifier OMICS_22502
Name PSAT
Alternative name Prokaryotic Sequence homology Analysis Tool
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Documentation


Maintainers


  • person_outline PSAT Team <>
  • person_outline Mitchell Brittnacher <>
  • person_outline Christine Fong <>
  • person_outline Laurence Rohmer <>
  • person_outline Matthew Radey <>

Additional information


http://www.nwrce.org/cgi-bin/psat/help_contents.cgi

Information


Unique identifier OMICS_22502
Name PSAT
Alternative name Prokaryotic Sequence homology Analysis Tool
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Perl
Database management system PostgreSQL
Computer skills Advanced
Stability Stable
Requirements Apache, PostgreSQL, PerlMagick
Maintained Yes

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Documentation


Maintainers


  • person_outline PSAT Team <>
  • person_outline Mitchell Brittnacher <>
  • person_outline Christine Fong <>
  • person_outline Laurence Rohmer <>
  • person_outline Matthew Radey <>

Additional information


http://www.nwrce.org/cgi-bin/psat/help_contents.cgi

Publication for Prokaryotic Sequence homology Analysis Tool

PSAT IN pipelines

 (2)
2016
PMCID: 4758666
PMID: 26890609
DOI: 10.1371/journal.pntd.0004403

[…] i/iii clusters, a custom postgresql database was created using the annotated genomes of 20 species. orthologs were identified with blastp (-f “m s” -s t) and conserved genomic neighborhood using the prokaryotic sequence homology analysis tool (psat) [77]., the genomes of 17 leptospira spp. isolates were newly determined for this study, representing 8 pathogenic, 4 intermediate and 5 saprophytic […]

2016
PMCID: 4758666
PMID: 26890609
DOI: 10.1371/journal.pntd.0004403

[…] was created using the annotated genomes of 20 species. orthologs were identified with blastp (-f “m s” -s t) and conserved genomic neighborhood using the prokaryotic sequence homology analysis tool (psat) [77]., the genomes of 17 leptospira spp. isolates were newly determined for this study, representing 8 pathogenic, 4 intermediate and 5 saprophytic clades and used in pan-genomic comparative […]

PSAT institution(s)
Department of Genome Sciences, University of Washington, Seattle, WA, USA
PSAT funding source(s)
Supported by the NIH, NIAID award for the Northwest RCE (NWRCE), grant U54AIO57141.

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