A tutorial of recent developments in the seeding of local alignment

J Bioinform Comput Biol. 2004 Dec;2(4):819-42. doi: 10.1142/s0219720004000983.

Abstract

We review recent results on local alignment. We begin with a review of classical methods and early heuristic methods, and then focus on more recent work on the seeding of local alignment. We show that these techniques give a vast improvement in both sensitivity and specificity over previous methods, and can achieve sensitivity at the level of classical algorithms while requiring orders of magnitude less runtime.

Publication types

  • Comparative Study
  • Evaluation Study
  • Research Support, Non-U.S. Gov't
  • Review

MeSH terms

  • Algorithms*
  • Computer Simulation
  • Databases, Genetic
  • Models, Genetic*
  • Models, Statistical
  • Pattern Recognition, Automated / methods*
  • Pattern Recognition, Automated / trends
  • Reproducibility of Results
  • Sensitivity and Specificity
  • Sequence Alignment / methods*
  • Sequence Alignment / trends
  • Sequence Analysis / methods*
  • Sequence Analysis / trends
  • Sequence Homology