Finding the most significant common sequence and structure motifs in a set of RNA sequences.

@article{Gorodkin1997FindingTM,
  title={Finding the most significant common sequence and structure motifs in a set of RNA sequences.},
  author={Jan Gorodkin and Laurie J. Heyer and Gary D. Stormo},
  journal={Nucleic acids research},
  year={1997},
  volume={25 18},
  pages={3724-32}
}
We present a computational scheme to locally align a collection of RNA sequences using sequence and structure constraints. In addition, the method searches for the resulting alignments with the most significant common motifs, among all possible collections. The first part utilizes a simplified version of the Sankoff algorithm for simultaneous folding and alignment of RNA sequences, but maintains tractability by constructing multi-sequence alignments from pairwise comparisons. The algorithm… CONTINUE READING
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