Lik Mui, More testing reveals that the -Y option works as follows. In the absense of -Y, the "effective search space" is the product of the query sequence length and the total database length. It affects the calculation of the expection value but not the score. It will thus vary with the query sequence length. Using "-Y 12345" sets the above "effective search space" to 12345, constant for each query sequence. To make the expectation roughly reflect match length, one could use a -Y value that is the product of the database size and the longest query sequence size. Pam and Bill