Direct RNA motif definition and identification from multiple sequence alignments using secondary structure profiles.

@article{Gautheret2001DirectRM,
  title={Direct RNA motif definition and identification from multiple sequence alignments using secondary structure profiles.},
  author={Daniel Gautheret and Aric B. Lambert},
  journal={Journal of molecular biology},
  year={2001},
  volume={313 5},
  pages={1003-11}
}
We present here a new approach to the problem of defining RNA signatures and finding their occurrences in sequence databases. The proposed method is based on "secondary structure profiles". An RNA sequence alignment with secondary structure information is used as an input. Two types of weight matrices/profiles are constructed from this alignment: single strands are represented by a classical lod-scores profile while helical regions are represented by an extended "helical profile" comprising 16… CONTINUE READING
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