[ensembl-dev] [SPAM] - Re: Different chromosome names - Bayesian Filter detected spam

[Oliver, Gavin]

Cheers Neil!

That explains things.  I guess I'll keep these in my database.

Gavin

-----Original Message-----
From: Neil Walker [mailto:neil.walker at cimr.cam.ac.uk] 
Sent: 23 November 2010 14:41
To: Oliver, Gavin
Cc: dev; neil.walker at cimr.cam.ac.uk
Subject: [SPAM] - Re: [ensembl-dev] Different chromosome names -
Bayesian Filter detected spam

Hi Gavin

> I have noticed that Havana genes etc seem to annotate a different
format 
> of chromosome name e.g. HSCHR6_MHC_DBB.
> 
>  
> 
> Simply out of curiosity can someone tell me why this occurs?

By coincidence, we were looking at this yesterday:

http://www.ensembl.org/Homo_sapiens/Info/Content?file=haplotypes.html

Basically, some regions of the genome are so polymorphic *and*
important, that a few alternative named haplotypes have been assembled.

I'd actually quite like to know where this is going under the influence
of the 1000 Genomes - is the *whole* genome going to get these
alternative haplotypes, or is there some other cunning plan to represent
relative and absolute positions?

Cheers
Neil

-- 
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Neil Walker                         email: neil.walker at cimr.cam.ac.uk
JDRF/WT Diabetes and Inflammation   tel: +44 (0)1223 763210
	Laboratory		    fax: +44 (0)1223 762102
Cambridge, UK                    http://www-gene.cimr.cam.ac.uk/todd/
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