One-to-one alignments
Martin Gollery wrote:
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
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