[BiO BB] time efficient global alignment algorithm

[Ryan Golhar]

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 <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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> 
> 
>