Finding weak motifs in DNA sequences.
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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.
author list (cited authors)
Sze, S. H., Gelfand, M. S., & Pevzner, P. A.
complete list of authors
Sze, SH||Gelfand, MS||Pevzner, PA