pfsearchV3
Computational Tool
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General Information
DescriptionA code acceleration and heuristic to search PROSITE profiles
Homepagehttp://web.expasy.org/pftools/#pfsearchV3
Publications
pfsearchV3: a code acceleration and heuristic to search PROSITE profiles
Thierry Schuepbach; Marco Pagni; Alan Bridge; Lydie Bougueleret; Ioannis Xenarios; Lorenzo Cerutti
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.
Contact: pftools@isb-sib.ch
DOI: https://doi.org/10.1093/bioinformatics/btt129
Metrics:
3
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