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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