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Title: Good spaced seeds for homology search
Authors: Choi, K.P. 
Zeng, F.
Zhang, L. 
Issue Date: 1-May-2004
Citation: Choi, K.P., Zeng, F., Zhang, L. (2004-05-01). Good spaced seeds for homology search. Bioinformatics 20 (7) : 1053-1059. ScholarBank@NUS Repository.
Abstract: 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. © Oxford University Press 2004; all rights reserved.
Source Title: Bioinformatics
ISSN: 13674803
DOI: 10.1093/bioinformatics/bth037
Appears in Collections:Staff Publications

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