[EMBOSS] Align 12bp DNA back to genome

[Magdy Alabady]

Hi,
I have used GMap to exactly what you are asking for but with little longer
reads (sRNA). It worked well. You might want to try
GMap<http://www.gene.com/share/gmap/>.

magdy

On Fri, Feb 6, 2009 at 10:42 AM, Peter Rice <pmr at ebi.ac.uk> wrote:

> 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
>
> _______________________________________________
> EMBOSS mailing list
> EMBOSS at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/emboss
>



-- 
--------------------------------------------------------
Magdy S. Alabady, PhD
Energy Bioscience Institute (EBI)
Institute for Genome Biology (IGB)
University of Illinois At Urbana-Champaign, Illinois
------------------------------------------------------
Imagination is more important than knowledge. For knowledge is limited,
whereas imagination embraces the entire world, stimulating progress, giving
birth to evolution.. .....Albert Einstein
-------------------------------------------------------------