[EMBOSS] Many-to-many with needle and water

[Peter Rice]

Hi Stefanie,

lueck at ipk-gatersleben.de wrote:
> Hi!
> 
> I would be interested in "superneedle" if the speed is acceptable. I'm
> still looking for a fast and good enough short sequence finder/aligner
> (see
> http://www.mailinglistarchive.com/biopython@biopython.org/msg00941.html).
> 
> At the moment I'm still using BLAST because I have no time to switch but
> later I would like to change to another algorithm.

>From the biopython message it seems you mainly want to find exact 21-mers.

Can you give an example of a query and a database so I can test the
speed of current EMBOSS applications like wordfinder

regards,

Peter Rice