[BioPython] fast pairwise alignment

[michael schmitt]

Hello. 

I want to align pairs of amino acid sequences, using
affine gap costs and a blosum62 substitution matrix.
Currently I use pairwise2.align.globaldd, but this is
quite slow (1-3 seconds per pair with sequences of 100
to 400 amino acids). As I want to do a larger
all-vs-all comparison, this is not feasible.

So
1) As I can import cpairwise2, I assume that this is
used for aligment. I also use the one_aligment_only
option. Is there another way to speed this up? Does
the implementation make use of the fact, that the gap
costs are affine, not arbitrary?

2) Are there external programs, which provide fast
pairwise algnments with the above requirements, that
could be used via the fasta interface?

3) What comparison time do you expect for two "normal"
protein sequences. Maybe I just underestimate the time
necessary for this.

Thanks for any hints.
Best regards, 
Michael


	

	
		
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