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JCB
2007

Clustered Sequence Representation for Fast Homology Search

9 years 2 months ago
Clustered Sequence Representation for Fast Homology Search
We present a novel approach to managing redundancy in sequence databanks such as GenBank. We store clusters of near-identical sequences as a representative union-sequence and a set of corresponding edits to that sequence. During search, the query is compared to only the union-sequences representing each cluster; cluster members are then only reconstructed and aligned if the union-sequence achieves a sufficiently high score. Using this approach with BLAST results in a 27% reduction in collection size and a corresponding 22% decrease in search time with no significant change in accuracy. We also describe our method for clustering that uses fingerprinting, an approach that has been successfully applied to collections of text and web documents in Information Retrieval. Our clustering approach is ten times faster on the GenBank nonredundant protein database than the fastest existing approach, CD-HIT. We have integrated our approach into FSA-BLAST, our new Open Source version of BLAST (a...
Michael Cameron, Yaniv Bernstein, Hugh E. Williams
Added 15 Dec 2010
Updated 15 Dec 2010
Type Journal
Year 2007
Where JCB
Authors Michael Cameron, Yaniv Bernstein, Hugh E. Williams
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