Journal
BIOINFORMATICS
Volume 20, Issue 16, Pages 2529-2533Publisher
OXFORD UNIV PRESS
DOI: 10.1093/bioinformatics/bth279
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Funding
- NHGRI NIH HHS [R01 HG01502, R01 HG01676] Funding Source: Medline
- NIGMS NIH HHS [4R33 GM066400] Funding Source: Medline
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Motivation: Studies of efficient and sensitive sequence comparison methods are driven by a need to find homologous regions of weak similarity between large genomes. Results: We describe an improved method for finding similar regions between two sets of DNA sequences. The new method generalizes existing methods by locating word matches between sequences under two or more word models and extending word matches into high-scoring segment pairs (HSPs). The method is implemented as a computer program named DDS2. Experimental results show that DDS2 can find more HSPs by using several word models than by using one word model.
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