[EMBOSS] Align 12bp DNA back to genome

[Peter Rice]

Aengus Stewart wrote:
> After trimming a bunch of illumina reads I have sequences that are 12bp 
> long and "we" want to find their genomic location

Can you say that they should match exactly (depending on the size of 
genome, and the accuracy of the reads)?

A word matching algorithm should work well.

How many reads do you have?

This is actually a problem we are very interested in writing EMBOSS 
applications for.

regards,

Peter