An experimental study of compressed indexing and local alignments of DNA

Authors:
Tak-Wah Lam;Wing-Kin Sung;Siu-Lung Tam;Chi-Kwong Wong;Siu-Ming Yiu
Affiliations:
Department of Computer Science, University of Hong Kong, Hong Kong;Department of Computer Science, National University of Singapore, Singapore;Department of Computer Science, University of Hong Kong, Hong Kong;Department of Computer Science, University of Hong Kong, Hong Kong;Department of Computer Science, University of Hong Kong, Hong Kong
Venue:
COCOA'07 Proceedings of the 1st international conference on Combinatorial optimization and applications
Year:
2007

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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 substrings 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.