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Bioinformatics Advance Access published online on February 5, 2004
Bioinformatics, doi:10.1093/bioinformatics/bth037
Bioinformatics © Oxford University Press 2004; all rights reserved
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Received October 7, 2003
Accepted November 15, 2003

Article

Good spaced seeds for homology search

Kwok Pui Choi 1, Fanfan Zeng 2, Louxin Zhang 3

1 Department of Mathematics, National University of Singapore, Singapore 117543; Department of Statistics and Applied Probability, NUS, Singapore 117543
2 School of Computing, NUS, Singapore 117543
3 Department of Mathematics, National University of Singapore, Singapore 117543


  Abstract

Motivation: Filtration is an important technique used to speed up local alignment as exemplified in the BLAST programs. Recently, Ma, Tromp and Li (2002) discovered that better filtering can be achieved by spacing out the matching positions according to a certain pattern, instead of contiguous positions to trigger a local alignment in their PatternHunter program. Such a match pattern is called a spaced seed.

Results: Our numerical computation shows that the ranks of spaced seeds (based on sensitivity) change with the sequences similarity. Since homologous sequences may have diverse similarity, we assess the sensitivity of spaced seeds over a range of similarity levels and present a list of good spaced seeds for facilitating homology search in DNA genomic sequences. We validate that the listed spaced seeds are indeed more sensitive using three arbitrarily chosen pairs of DNA genomic sequences.

Contact: matzlx@nus.edu.sg


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