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.
Keywords
BiologyDistribution (mathematics)Sequence (biology)StatisticsEstimation theoryStatistical modelStatistical parameterStatistical analysisStatistical physicsAlgorithmMathematicsBiological systemMathematical analysisPhysicsGenetics
MeSH Terms
AlgorithmsComputational BiologyLikelihood FunctionsSequence AlignmentSequence AnalysisProteinStatistical Distributions
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Publication Info
- Year
- 2001
- Type
- article
- Volume
- 29
- Issue
- 2
- Pages
- 351-361
- Citations
- 182
- Access
- Closed
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Cite This
Stephen F. Altschul
(2001).
The estimation of statistical parameters for local alignment score distributions.
Nucleic Acids Research
, 29
(2)
, 351-361.
https://doi.org/10.1093/nar/29.2.351
Identifiers
- DOI
- 10.1093/nar/29.2.351
- PMID
- 11139604
- PMCID
- PMC29669