PSI-Search: iterative HOE-reduced profile SSEARCH searching.
Bioinformatics
; 28(12): 1650-1, 2012 Jun 15.
Article
in En
| MEDLINE
| ID: mdl-22539666
ABSTRACT
UNLABELLED Iterative similarity searches with PSI-BLAST position-specific score matrices (PSSMs) find many more homologs than single searches, but PSSMs can be contaminated when homologous alignments are extended into unrelated protein domains-homologous over-extension (HOE). PSI-Search combines an optimal Smith-Waterman local alignment sequence search, using SSEARCH, with the PSI-BLAST profile construction strategy. An optional sequence boundary-masking procedure, which prevents alignments from being extended after they are initially included, can reduce HOE errors in the PSSM profile. Preventing HOE improves selectivity for both PSI-BLAST and PSI-Search, but PSI-Search has ~4-fold better selectivity than PSI-BLAST and similar sensitivity at 50% and 60% family coverage. PSI-Search is also produces 2- for 4-fold fewer false-positives than JackHMMER, but is ~5% less sensitive. AVAILABILITY AND IMPLEMENTATION PSI-Search is available from the authors as a standalone implementation written in Perl for Linux-compatible platforms. It is also available through a web interface (www.ebi.ac.uk/Tools/sss/psisearch) and SOAP and REST Web Services (www.ebi.ac.uk/Tools/webservices).
Full text:
1
Collection:
01-internacional
Database:
MEDLINE
Main subject:
Software
/
Sequence Alignment
/
Amino Acid Motifs
Language:
En
Journal:
Bioinformatics
Journal subject:
INFORMATICA MEDICA
Year:
2012
Document type:
Article
Affiliation country:
United kingdom