Comparative Study
doi: 10.1142/9789812799623_0022.
Finding weak motifs in DNA sequences
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- PMID: 11928479
- DOI: 10.1142/9789812799623_0022
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Comparative Study
Finding weak motifs in DNA sequences
Pac Symp Biocomput.
2002.
Free article
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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