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PubMed · 16100379

Using multiple alignments to improve seeded local alignment algorithms.

Jason Flannick·Serafim Batzoglou
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Abstract

Multiple alignments among genomes are becoming increasingly prevalent. This trend motivates the development of tools for efficient homology search between a query sequence and a database of multiple alignments. In this paper, we present an algorithm that uses the information implicit in a multiple alignment to dynamically build an index that is weighted most heavily towards the promising regions of the multiple alignment. We have implemented Typhon, a local alignment tool that incorporates our indexing algorithm, which our test results show to be more sensitive than algorithms that index only a sequence. This suggests that when applied on a whole-genome scale, Typhon should provide improved homology searches in time comparable to existing algorithms.

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AlgorithmsAnimalsBase SequenceDatabases, Nucleic AcidGenomicsHumansSequence AlignmentSoftwareEvaluation StudyJournal ArticleResearch Support, N.I.H., ExtramuralResearch Support, Non-U.S. Gov'tResearch Support, U.S. Gov't, Non-P.H.S.Research Support, U.S. Gov't, P.H.S.

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Jason Flannick, Serafim Batzoglou. 2005-08-12. Using multiple alignments to improve seeded local alignment algorithms.. https://doi.org/10.1093/nar%2Fgki767

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