Parallel and Distributed Processing Symposium, International (2008)
Miami, FL, USA
Apr. 14, 2008 to Apr. 18, 2008
Dominique Lavenier , IRISA / CNRS, Campus de Beaulieu, 35042 Rennes, France
This paper presents a seed-based algorithm for intensive DNA sequence comparison. The novelty comes from the way seeds are used to efficiently generate small ungapped alignments - or HSPs (High Scoring Pairs) - in the first stage of the search. W-nt words are first indexed and all the 4W possible seeds are enumerated following a strict order ensuring fast generation of unique HSPs. A prototype - written in C - has been realized and tested on large DNA banks. Speed-up compared to BLASTN range from 5 to 28 with comparable sensitivity.
Dominique Lavenier, "Ordered index seed algorithm for intensive DNA sequence comparison", Parallel and Distributed Processing Symposium, International, vol. 00, no. , pp. 1-8, 2008, doi:10.1109/IPDPS.2008.4536172