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Bioinformatics Advance Access originally published online on February 5, 2004
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Bioinformatics 20(7) © Oxford University Press 2004; all rights reserved.

Good spaced seeds for homology search

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

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

Received on October 7, 2003; revised on October 7, 2003; accepted on November 15, 2003
Advance Access Publication February 12, 2004

Motivation: Filtration is an important technique used to speed up local alignment as exemplified in the BLAST programs. Recently, Ma et al. 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{at}nus.edu.sg

* To whom correspondence should be addressed.


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