The estimation of statistical parameters for local alignment score distributions

The distribution of optimal local alignment scores of random sequences play s a vital role in evaluating the statistical significance of sequence align ments, 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 analytical ly, but must be estimated by curve fitting. For obtaining accurate paramete r estimates, a form of the recently described 'island' method has several a dvantages. We describe this method in detail, and use it to investigate the functional dependence of these parameters on finite-length edge effects.