Format

Send to

Choose Destination
See comment in PubMed Commons below
Bioinformatics. 2013 May 1;29(9):1215-7. doi: 10.1093/bioinformatics/btt129. Epub 2013 Mar 16.

pfsearchV3: a code acceleration and heuristic to search PROSITE profiles.

Author information

1
Vital-IT Group, SIB Swiss Institute of Bioinformatics, Genopode, UNIL-Sorge, 1015 Lausanne, Switzerland.

Abstract

SUMMARY:

The PROSITE resource provides a rich and well annotated source of signatures in the form of generalized profiles that allow protein domain detection and functional annotation. One of the major limiting factors in the application of PROSITE in genome and metagenome annotation pipelines is the time required to search protein sequence databases for putative matches. We describe an improved and optimized implementation of the PROSITE search tool pfsearch that, combined with a newly developed heuristic, addresses this limitation. On a modern x86_64 hyper-threaded quad-core desktop computer, the new pfsearchV3 is two orders of magnitude faster than the original algorithm.

AVAILABILITY AND IMPLEMENTATION:

Source code and binaries of pfsearchV3 are freely available for download at http://web.expasy.org/pftools/#pfsearchV3, implemented in C and supported on Linux. PROSITE generalized profiles including the heuristic cut-off scores are available at the same address.

PMID:
23505298
PMCID:
PMC3634184
DOI:
10.1093/bioinformatics/btt129
[Indexed for MEDLINE]
Free PMC Article
PubMed Commons home

PubMed Commons

0 comments
How to join PubMed Commons

    Supplemental Content

    Full text links

    Icon for Silverchair Information Systems Icon for PubMed Central
    Loading ...
    Support Center