Hello, I am getting a weird problem with protein alignment using NeedlemanWunsch in 1.7.1, in that the alignment does not span the entire length of the proteins. I've verified that this should not happen with needle (from EMBOSS), neobio, BioJava3, and NW on NCBI. I'm reluctant to switch to BioJava3 at this time, since performance is about 2-3x slower than 1.7.1 for the alignments, and I'm doing about 350,000 of them.
An example of this alignment error, is shown here: http://pastebin.com/mdX516R6 Notice that the alignment stops 1 amino acid short of the end in both cases. The parameters for the alignment are: BLOSUM50, gapOpen=10, gapExtend=2. Thanks, Chris -- PhD Candidate, Integrative Life Sciences Virginia Commonwealth University Richmond, VA _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l
