[BiO BB] time efficient global alignment algorithm

[Ryan Golhar]

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