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 <[email protected]> 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 > [email protected] > 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 ------------------------------------------------------------- _______________________________________________ EMBOSS mailing list [email protected] http://lists.open-bio.org/mailman/listinfo/emboss
