Hi Chris, about your comment that the biojava3-alignment is slower than the 1.7 one: Do you have any data if this is coming from the io or is the actual alignment calculation slower?
Andreas On Sun, Oct 24, 2010 at 7:57 AM, Chris Friedline <[email protected]> wrote: > 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 > -- ----------------------------------------------------------------------- Dr. Andreas Prlic Senior Scientist, RCSB PDB Protein Data Bank University of California, San Diego (+1) 858.246.0526 ----------------------------------------------------------------------- _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l
