[EMBOSS] Align 12bp DNA back to genome

[Lapointe, David]

Aengus,

You might try looking here for other software. Maq, soap, rmap, etc are
relatively fast but still time-consuming.

http://seqanswers.com/forums/showthread.php?t=43

David

-----Original Message-----
From: emboss-bounces at lists.open-bio.org
[mailto:emboss-bounces at lists.open-bio.org] On Behalf Of Aengus Stewart
Sent: Friday, February 06, 2009 11:11 AM
To: emboss at lists.open-bio.org
Subject: [EMBOSS] Align 12bp DNA back to genome


Hi all,

This isnt an EMBOSS question per se but I thought it would go to the
right audience.

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

Before anyone even says "Why do you want to do that?" can I suggest

1) Treat it as a hypothetical case
2) because the scientist who asked me wants it

:-)

I have both a perl regex and fuzznuc running now for oh about a
week..........

I have also attempted to build/configure/run without success

maq
soap
blat

So can anyone suggest anything else to try (probably I have missed the
obvious) before the regex and 
fuzznuc finish?

This completes the Friday pm puzzler........



Cheers
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