title: Finding weak motifs in DNA sequences.
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.
authors.affiliation: Department of Computer Science and Engineering, University of California at San Diego, La Jolla, CA 92093-0114, USA.
authors.forename: S H
authors.initials: SH
authors.lastname: Sze
authors.forename: M S
authors.initials: MS
authors.lastname: Gelfand
authors.forename: P A
authors.initials: PA
authors.lastname: Pevzner
mesh_terms: D001483:Base Sequence; D019295:Computational Biology / Q000379:methods; D004247:DNA / Q000737:chemistry* / Q000235:genetics*; D015870:Gene Expression; D012045:Regulatory Sequences, Nucleic Acid; D015203:Reproducibility of Results; D012984:Software
chemical_list: D004247:DNA