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Nucleic Acids Research, 2001, Vol. 29, No. 2 351-361
© 2001 Oxford University Press

The estimation of statistical parameters for local alignment score distributions

Stephen F. Altschul*, Ralf Bundschuh1, Rolf Olsen1 and Terence Hwa1

National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA and 1Department of Physics, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0319, USA

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.

* To whom correspondence should be addressed. Tel: +1 301 496 2475; Fax: +1 301 480 9241; Email: altschul{at}ncbi.nlm.nih.gov


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