Work

The estimation of statistical parameters for local alignment score distributions

Year: 2001

Type: article

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.

Source: Nucleic Acids Research

DOI: 10.1093/nar/29.2.351

Author: S. F. Altschul

Institutions: National Institutes of Health, National Center for Biotechnology Information

Language: English

Topic: Genomics and Phylogenetic Studies

Subfield: Molecular Biology

Field: Biochemistry, Genetics and Molecular Biology

Domain: Life Sciences

Open Access status: bronze

Funders: National Science Foundation, Wellcome Trust, Deutscher Akademischer Austauschdienst, Division of Materials Research

Awards: Statistical Mechanics of Sequence Matching, Computational Laboratory for the Development of New Approaches to Complex Biological Phenomena