Finding weak motifs in DNA sequences.

S H Sze; M S Gelfand; P A Pevzner

doi:10.1142/9789812799623_0022

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Finding weak motifs in DNA sequences.

S H Sze·M S Gelfand·P A Pevzner

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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.

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Base Sequence Computational Biology DNA Gene Expression Regulatory Sequences, Nucleic Acid Reproducibility of Results Software Comparative Study Journal Article Research Support, Non-U.S. Gov't

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S H Sze, M S Gelfand, P A Pevzner. 2002. Finding weak motifs in DNA sequences.. https://doi.org/10.1142/9789812799623_0022

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