Ordered index seed algorithm for intensive DNA sequence comparison

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.

• Type: Conference
• Year: 2008
• Where: IPPS
• Authors: Dominique Lavenier
• Keywords: Distributed And Parallel Computing, Intensive Dna Sequence, IPPS 2008, Small Ungapped Alignments, first Stage