StrAl: progressive alignment of non-coding RNA using base pairing probability vectors in quadratic time

@article{Dalli2006StrAlPA,
  title={StrAl: progressive alignment of non-coding RNA using base pairing probability vectors in quadratic time},
  author={Deniz Dalli and A. Wilm and Indra Mainz and G. Steger},
  journal={Bioinformatics},
  year={2006},
  volume={22 13},
  pages={
          1593-9
        }
}
MOTIVATION Alignment of RNA has a wide range of applications, for example in phylogeny inference, consensus structure prediction and homology searches. Yet aligning structural or non-coding RNAs (ncRNAs) correctly is notoriously difficult as these RNA sequences may evolve by compensatory mutations, which maintain base pairing but destroy sequence homology. Ideally, alignment programs would take RNA structure into account. The Sankoff algorithm for the simultaneous solution of RNA structure… Expand
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