Hello, I'm looking for a source related to optimal alignments with an affine gap penalty. I previously posted this request to BiO_Bulletin_Board and was referred here. Consider aligning 2 sequences with an affine gap penalty. The obvious method of using dynamic programming requires 3 matrices (or, equivalently, 3 values in each cell of a single matrix). One matrix will have values computed from the costs of subalignments ending with a gap in one of the sequences. Another of the matrices will have values computed from the cost of subalignments ending with a gap in the other sequence. The remaining matrix will result from subalignments that end without a gap in either sequence. Durbin, et al.'s Biological Sequence Analysis (1998) refers to an algorithm that uses only 2 matrices, one that results from subalignments ending in a gap in either sequence, and one that results from subalignments ending in a gap in neither sequence (pages 30-31). They claim that a constraint on the cost function will guarantee optimal results from this algorithm, only he offers no proof or citation. Certainly there is a paper that demonstrates this result, only I have been unable to find it. I would appreciate any information you may have on this, whether it is a citation or even an assurance that such a paper exists. Thanks, Alex