Brona Brejova, Daniel G. Brown, Tomas Vinar. Vector seeds: an extension to spaced seeds. Journal of Computer and System Sciences, 70(3):364-380. May 2005. Special issue on bioinformatics. Early version in WABI 2003.
Download preprint: 04jcss.pdf, 406Kb
Download from publisher: http://dx.doi.org/10.1016/j.jcss.2004.12.008
Related web page: not available
Bibliography entry: BibTeX
See also: early version
We present improved techniques for finding homologous regions in DNA and protein sequences. Our approach focuses on the core regions of a local pairwise alignment; we suggest new ways to characterize these regions that allow marked improvements in both specificity and sensitivity over existing techniques for sequence alignment. For any such characterization, which we call a vector seed, we give an e cient algorithm that estimates the specificity and sensitivity of that seed under reasonable probabilistic models of sequence. We also characterize the probability of a match when an alignment is required to have multiple hits before it is detected. Our extensions fit well with existing approaches to sequence alignment, while still offering substantial improvement in runtime and sensitivity, particularly for the important problem of identifying matches between homologous coding DNA sequences.