[BiO BB] time efficient global alignment algorithm

[Paulo Nuin]

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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