[EMBOSS] Align 12bp DNA back to genome

Peter Rice pmr at ebi.ac.uk
Fri Feb 6 16:42:27 UTC 2009


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



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