The estimation of statistical parameters for local alignment score distributions

Nucleic Acids Res. 2001 Jan 15;29(2):351-61. doi: 10.1093/nar/29.2.351.

Abstract

The distribution of optimal local alignment scores of random sequences plays a vital role in evaluating the statistical significance of sequence alignments. These scores can be well described by an extreme-value distribution. The distribution's parameters depend upon the scoring system employed and the random letter frequencies; in general they cannot be derived analytically, but must be estimated by curve fitting. For obtaining accurate parameter estimates, a form of the recently described 'island' method has several advantages. We describe this method in detail, and use it to investigate the functional dependence of these parameters on finite-length edge effects.

Publication types

  • Comparative Study

MeSH terms

  • Algorithms
  • Computational Biology / methods
  • Computational Biology / statistics & numerical data
  • Likelihood Functions
  • Sequence Alignment / methods
  • Sequence Alignment / statistics & numerical data*
  • Sequence Analysis, Protein / methods
  • Sequence Analysis, Protein / statistics & numerical data
  • Statistical Distributions*