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Oxford University Press (OUP), Bioinformatics, 9(29), p. 1215-1217

DOI: 10.1093/bioinformatics/btt129

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pfsearchV3: a code acceleration and heuristic to search PROSITE profiles

Journal article published in 2013 by Thierry Schuepbach, Marco Pagni, Alan Bridge, Lydie Bougueleret, Ioannis Xenarios ORCID, Lorenzo Cerutti
This paper is made freely available by the publisher.
This paper is made freely available by the publisher.

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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.