Finding optimal degenerate patterns in DNA sequences

@article{Shinozaki2003FindingOD,
  title={Finding optimal degenerate patterns in DNA sequences},
  author={Daisuke Shinozaki and Tatsuya Akutsu and Osamu Maruyama},
  journal={Bioinformatics},
  year={2003},
  volume={19 Suppl 2},
  pages={ii206-14}
}
MOTIVATION The problem of finding transcription factor binding sites in the upstream regions of given genes is algorithmically an interesting and challenging problem in computational biology. A degenerate pattern over a finite alphabet Sigma is a sequence of subsets of Sigma. A string over IUPAC nucleic acid codes is also a degenerate pattern over Sigma = {A, C, G, T}, and is used as one of the major patterns modeling transcription factor binding sites in the upstream regions of genes. However… CONTINUE READING
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