Optimal Spaced Seeds for Finding Homologous Coding Regions
BibTeX
@MISC{Brejov_optimalspaced,
author = {Bro Na Brejov and Daniel G. Brown},
title = {Optimal Spaced Seeds for Finding Homologous Coding Regions},
year = {}
}
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Abstract
We study the problem of computing optimal spaced seeds for identifying homologous coding DNA sequences in long sequence data sets. We develop two models of DNA sequence alignment in coding regions, and using data sets from human/Drosophila and human/mouse comparisons, we compute optimal spaced seeds using a dynamic programming algorithm. The seeds we identify are more sensitive by far at identifying homologous regions than the seeds from BLAST or from PatternHunter, and also signi cantly improve on the sensitivity of WABA, which also uses a simple spaced seed. In particular, in human/Drosophila comparisons, we oer an 82% improvement in false negatives over BLAST and a 33% improvement over WABA. Our results oer the hope of improved gene nding due to fewer missed exons in DNA/DNA comparison, and more eective homology search in general.
Citations
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