Finding weak motifs in DNA sequences.

S. H. Sze, M. S. Gelfand, P. A. Pevzner

Research output: Contribution to journalArticlepeer-review

21 Citations (Scopus)

Abstract

Recognition of regulatory sites in unaligned DNA sequences is an old and well-studied problem in computational molecular biology. Recently, large-scale expression studies and comparative genomics brought this problem into a spotlight by generating a large number of samples with unknown regulatory signals. Here we develop algorithms for recognition of signals in corrupted samples (where only a fraction of sequences contain sites) with biased nucleotide composition. We further benchmark these and other algorithms on several bacterial and archaeal sites in a setting specifically designed to imitate the situations arising in comparative genomics studies.

Original languageEnglish
Pages (from-to)235-246
Number of pages12
JournalPacific Symposium on Biocomputing. Pacific Symposium on Biocomputing
Publication statusPublished - 2002
Externally publishedYes

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