Protein Parameters

Two sets of substitution scores and gap penalties are used, one for DNA and cDNA sequences, and the other for protein sequences. If one or both sequences are protein sequences, then the values in the middle parameter panel are used by the alignment programs. In this case, the user can specify the score for each match and mismatch by selecting BLOSUM62 or PAM250 matrix. The user can also change the gap open penalty (a non-negative integer), and the gap extension penalty (a positive integer).