[BiO BB] time efficient global alignment algorithm

[Martin Gollery]

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 <golharam at umdnj.edu> 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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Martin Gollery
Senior Bioinformatics Scientist
Tahoe Informatics
www.bioinformaticist.biz
www.hiddenmarkovmodels.com