title: The estimation of statistical parameters for local alignment score distributions.
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.
authors.affiliation: National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA. altschul@ncbi.nlm.nih.gov
authors.forename: S F
authors.initials: SF
authors.lastname: Altschul
authors.forename: R
authors.initials: R
authors.lastname: Bundschuh
authors.forename: R
authors.initials: R
authors.lastname: Olsen
authors.forename: T
authors.initials: T
authors.lastname: Hwa
mesh_terms: D000465:Algorithms; D019295:Computational Biology / Q000379:methods / Q000706:statistics & numerical data; D016013:Likelihood Functions; D016415:Sequence Alignment / Q000379:methods / Q000706:statistics & numerical data*; D020539:Sequence Analysis, Protein / Q000379:methods / Q000706:statistics & numerical data; D016008:Statistical Distributions