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Pairwise alignment incorporating dipeptide covariation.

Gavin E Crooks1, Richard E Green, Steven E Brenner

  • 1Department of Plant and Microbial Biology 111 Koshland Hall #3102 University of California, Berkeley, CA 94720-3102, USA. gec@compbio.berkeley.edu

Bioinformatics (Oxford, England)
|August 27, 2005
PubMed
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Standard protein sequence alignment assumes independent residue evolution. This study found that incorporating local substitution correlations does not significantly improve remote homology detection, validating the standard assumption.

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Molecular Evolution

Background:

  • Pairwise protein sequence alignment typically assumes independent amino acid substitutions at neighboring sites.
  • This simplification enables fast alignment algorithms but may overlook information beneficial for remote homolog detection.

Purpose of the Study:

  • To investigate the validity of the independence assumption in protein sequence alignment.
  • To develop and evaluate an alignment algorithm incorporating local substitution correlations for enhanced remote homology detection.

Main Methods:

  • Construction of extended substitution matrices capturing neighboring site correlations.
  • Development of an efficient alignment algorithm integrating local substitution correlations.
  • Assessment of the algorithm's performance in detecting remote homologies.

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Main Results:

  • Analysis revealed that average local substitution correlations are not strong.
  • Incorporating local substitution correlations did not yield statistically significant improvements in remote homology detection.

Conclusions:

  • The standard assumption of independent residue evolution in protein sequences is an efficient and appropriate approximation.
  • Current alignment algorithms based on this assumption are effective for remote homology detection.