[Genome] chicken chromosome lengths

[Paul Flicek]

Hi Carl,

As an additional point, Ensembl will be providing the new Chicken  
assembly in the December release.  This release will be based on the  
WASHUC 2.1 assembly (aka galGal3) and include a new genebuild and a  
new variation database with dbSNP125 data.

The December Ensembl release is planned for either next Wednesday or  
Monday 18 December.

I hope this helps and please let us know if you have additional  
questions,

Paul

__
Paul Flicek, D.Sc.
Ensembl Functional Genomics Project Leader
EMBL-European Bioinformatics Institute
Wellcome Trust Genome Campus, Hinxton
Cambridge CB10 1SD, United Kingdom

Tel: +44 (0) 1223 492581
Fax: +44 (0) 1223 494468
http://www.ensembl.org


On 4 Dec 2006, at 18:13, Kayla Smith wrote:

> Carl,
>
> You are correct in assuming that the discrepancy you have observed is
> related to which build you are looking at.   We actually offer two
> different assemblies of the Chicken Browser:  galGal2 (Feb 2004) and
> galGal3 (May 2006).  From the data you have pasted below, it looks  
> like
> you were viewing our galGal3 browser (this is the default) and  
> comparing
> it to Ensembl's equivalent of the galGal2 assembly.
>
> On the gateway page, http://genome.ucsc.edu/cgi-bin/hgGateway, you can
> toggle between galGal2 and galGal3.  Each assembly has a "sequences"
> link which will give you information on the length of each chromosome.
>
> GalGal3:
> chr1:  200,994,015
> chr27:  4,841,970
>
> GalGal2:
> chr1:  188,239,860
> chr27:  2,668,888
>
>
> I hope this helps to answer your question.  Please don't hesitate to
> contact us again if you require further assistance.
>
> Kayla Smith
> UCSC Genome Bioinformatics Group
>
>
> Carl Schmidt wrote:
>> For the chicken, why are there differences in the total size of
>> chromosomes when I compare between UCSC and Ensembl?  I suppose it
>> has something to do with the build, but I am concerned about trying
>> to use coordinates in from one browser to access information in the
>> other.
>>   For example:
>> CH1	UCSC 200,994,015				ENSEMBL 188,239,860  	
>> CH 27 	UCSC:4,841,970					ENSEMBL: 2,668,888
>>
>>
>>
>> Carl J. Schmidt
>> Associate Professor
>> Department of Animal & Food Sciences
>> 051 Townsend Hall
>> University of Delaware
>> Newark, DE 19716-2150
>>
>> schmidtc at udel.edu
>> 302-831-1334
>> Fax: 302-831-2822
>> http://udel.edu/~schmidtc
>>
>>
>> _______________________________________________
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>
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