Aligning Protein Sequences with Predicted Secondary Structure

  title={Aligning Protein Sequences with Predicted Secondary Structure},
  author={John D. Kececioglu and Eagu Kim and Travis J. Wheeler},
  journal={Journal of computational biology : a journal of computational molecular cell biology},
  volume={17 3},
Accurately aligning distant protein sequences is notoriously difficult. Since the amino acid sequence alone often does not provide enough information to obtain accurate alignments under the standard alignment scoring functions, a recent approach to improving alignment accuracy is to use additional information such as secondary structure. We make several advances in alignment of protein sequences annotated with predicted secondary structure: (1) more accurate models for scoring alignments, (2… CONTINUE READING


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