Maximum-likelihood estimation of the statistical distribution of Smith-Waterman local sequence similarity scores - Mott, R. (Elsevier)
A method is described for estimating the distribution and hence testing the statistical significance of sequence similarity scores obtained during a data-bank search. Maximum-likelihood is used to fit a model to the scores, avoiding any costly simulation of random sequences. The method is applied in detail to the Smith-Waterman algorithm when gaps are allowed, and is shown to give results very similar to those obtained by simulation.
http://dx.doi.org/10.1016/S0092-8240(05)80176-4
Keywords: W; SA-SP