Hi David, There may be people on the list with dedicated sw code. I always use the BioJava dynamic programming library for this sort of thing. However, currently it only returns the optimal alignment. Sub-optimal alignments are definitely on my to-do list, but won't happen within the next month.
Matthew --- David Nix <[EMAIL PROTECTED]> wrote: > Hello Folks, > I'm looking for a local alignment script that > uses a variant of the > Smith-Waterman algorithm where, in addition to the > highest scoring > alignment, all other alignments above a given score > cut off are returned. > Two such programs have already been written in C > (LALIGN and SIM), but I > would like to use all native code in my application > to preserve the Java > portability. Any suggestions? -cheers, Dave > > > -- > David Austin Nix, PhD > University of California at Berkeley > Lawrence Berkeley National Lab > Mailstop 84-171 > One Cyclotron Road > Berkeley, CA 94720-3200 > > 510-486-6791 (lab) > 510-786-549-0137 (fax) > [EMAIL PROTECTED] > > > _______________________________________________ > Biojava-l mailing list - [EMAIL PROTECTED] > http://biojava.org/mailman/listinfo/biojava-l ________________________________________________________________________ Want to chat instantly with your online friends? Get the FREE Yahoo! Messenger http://uk.messenger.yahoo.com/ _______________________________________________ Biojava-l mailing list - [EMAIL PROTECTED] http://biojava.org/mailman/listinfo/biojava-l
