Ryan, are you trying to do lots of one-to-one alignments, or one very large multiple sequence alignment? Marty
On Mon, Aug 3, 2009 at 10:45 AM, Ryan Golhar <[email protected]> wrote: > I'm trying to perform a large amount of sequence alignments of long DNA > sequences, some up to 163,000+ bp in length. I was trying to use the > standard Needleman-Wunsch algorithm, but the matrix used requires a large > amount of memory...about 100 GB of memory. This obviously won't work. > > I tried using stretcher from the EMBOSS package, but it takes way too long > to align each pair of sequences. I'm looking for something that can perform > alignments fast using a reasonable amount of memory. > > I found one tool, called AVID, but have been unsuccessful in getting it to > run to the sequence set I have. > > Before I go an try to develop a new solution to this, does anyone have or > recommend a program to perform a large number of global pairwise alignments > for long sequences? > > Ideally, something with the speed similar to BLAST. > > Ryan > > _______________________________________________ > BBB mailing list > [email protected] > http://www.bioinformatics.org/mailman/listinfo/bbb > -- -- Martin Gollery Senior Bioinformatics Scientist Tahoe Informatics www.bioinformaticist.biz www.hiddenmarkovmodels.com _______________________________________________ BBB mailing list [email protected] http://www.bioinformatics.org/mailman/listinfo/bbb
