Hi
MUMMer never failed me. Check at
http://mummer.sourceforge.net/
HTH
Paulo
On 3-Aug-09, at 1:45 PM, Ryan Golhar 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
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