Ordered Index Seed Algorithm for Intensive DNA Sequence Comparison

International audienceThis 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 4^W 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