Finding weak motifs in DNA sequences.
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.
Sze
S H
SH
Department of Computer Science and Engineering, University of California at San Diego, La Jolla, CA 92093-0114, USA.
Gelfand
M S
MS
Pevzner
P A
PA
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
D004247:DNA