I was reading the paper "Maximum Likelihood Estimation of the Statistical distribution of Smith-Waterman Local Sequence Similarity Scores", published in Bulletin of Mathematical Biology Vol54, No1, p59-75 by R. Mott, and the paper "Sequence Comparison Significance and Poisson Approximation" published in Statistical Science vol9, 1994, 367-381,by M.S.Waterman et al. These articles discuss the ML method for estimating parameters for distributions obtained by searching a random sequence with a databank.It can be assumed that the sequences in the databank are independent sequences, but if we are using the same sequence as query each time,wouldn't the scores obtained be dependent? then the likelihood needs to be modified to account for this dependency? both of these papers used the likelihood assuming all the scores obtained are independent. Am I missing something here? Could someone please help me understand? Thanks very much. Lily __________________________________ Do you Yahoo!? New and Improved Yahoo! Mail - Send 10MB messages! http://promotions.yahoo.com/new_mail