An experimental study of compressed indexing and local alignments of DNA

Abstract

Recent experimental studies on compressed indexes (BWT, CSA, FM-index) have confirmed their practicality for indexing long DNA sequences such as the human genome (about 3 billion characters) in the main memory [5,13,16]. However, these indexes are designed for exact pattern matching, which is too stringent for most biological applications. The demand is often on finding local alignments (pairs of similar sub-strings with gaps allowed). In this paper, we show how to build a software called BWT-SW that exploits a BWT index of a text T to speed up the dynamic programming for finding all local alignments with any pattern P. Experiments reveal that BWT-SW is very efficient (e.g., aligning a pattern of length 3,000 with the human genome takes less than a minute). We have also analyzed BWT-SW mathematically, using a simpler model (with gaps disallowed) and random strings. We find that the expected running time is O(|T| 0,628|P|). As far as we know, BWT-SW is the first practical tool that can find all local alignments. © Springer-Verlag Berlin Heidelberg 2007.