[EMBOSS] Align 12bp DNA back to genome

[Magdy Alabady]

I haven't use bowite before, sorry. I used GMap extensivly to map sRNA to
genomes like rice, and it works fine. bear in mind that sRNA is around 20
bp. I don't a problem in your case, but a trial is needed to judge it


On Fri, Feb 6, 2009 at 11:12 AM, Aengus Stewart <
aengus.stewart at cancer.org.uk> wrote:

>
> hmmmmmm
>
> bowtie is on the list to build and test, but not for this problem.
>
> Can you assure me that both bowtie and GMap will work with 12bp sequences?
>
>
> Regards
>
> Aengus
>
> --
> -----------------------------------------------------------------------
> Aengus Stewart
> Head of Bioinformatics and BioStatistics
> Bioinformatics and BioStatistics               Tel: +44 (0)20 7269 3679
> Cancer Research UK, Lincoln's Inn Fields, Holborn, London, WC2A 3PX, UK
> -----------------------------------------------------------------------
>
> This electronic message contains information which may be privileged and
> confidential.  The information is intended to be for the use of the
> individual(s) or entity named above. Be aware that any third party
> disclosure, distribution, copying or use of this communication, without
> prior permission, is strictly prohibited.
>
> This communication is from Cancer Research UK. Our website is at
> www.cancerresearchuk.org. We are a charity registered under number 1089464
> and a company limited by guarantee registered in England & Wales under
> number 4325234. Our registered address is 61 Lincoln's Inn Fields, London
> WC2A 3PX. Our central telephone number is 020 7242 0200.
>
> This communication and any attachments contain information which is
> confidential and may also be privileged.   It is for the exclusive use of
> the intended recipient(s).  If you are not the intended recipient(s) please
> note that any form of disclosure, distribution, copying or use of this
> communication or the information in it or in any attachments is strictly
> prohibited and may be unlawful.  If you have received this communication in
> error, please notify the sender and delete the email and destroy any copies
> of it.
>
> E-mail communications cannot be guaranteed to be secure or error free, as
> information could be intercepted, corrupted, amended, lost, destroyed,
> arrive late or incomplete, or contain viruses.  We do not accept liability
> for any such matters or their consequences.  Anyone who communicates with us
> by e-mail is taken to accept the risks in doing so.
> _______________________________________________
> 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
-------------------------------------------------------------