[Gramene] Re: TAIR9 vs TAIR10 - mixup on naming, was: RE: Old versions?

[Jonathan Warren]

Hi

The DAS Registry automatically takes it's information from the gramene  
DAS sources document http://dev.gramene.org/gramenedas/das/sources. If  
the reference coordinates are the same then the coordinate system  
should remain as TAIR 9. However if there are new sequences added then  
new entry_points need to be added to a the DAS reference sources. If  
the gramene sources document reverts to TAIR 9 then the registry will  
automatically reflect this. As all the data sources using the TAIR 10  
coordinate system are gramenes no other problems should arise.

On 28 Jun 2011, at 15:26, Loraine, Ann wrote:

> Greetings all,
>
> There is some confusion about the meaning of TAIR9 versus TAIR10.
>
> TAIR9 is both a genome assembly release and a genome annotation  
> release, meaning: it includes both new sequences for Arabidopsis  
> chromosomes and some revised gene models.
>
> TAIR10 is a genome annotation release only. The chromosomes did not  
> change from TAIR9 to TAIR10 according to this README file:
>
> ftp://ftp.arabidopsis.org/home/tair/Sequences/whole_chromosomes/README_whole_chromosomes.txt
>
> quote*Please note that the chromosome files have NOT CHANGED FROM  
> TAIR9 to TAIR10*unquote
>
> Thus, the gene structure annotations released in TAIR10 are using  
> the same reference sequence as the gene structure annotations  
> released with TAIR9.
>
> I've noticed the DAS registry contains both TAIR9 and TAIR10 as  
> reference assembles and that some data sets (looks like alignments)  
> are referencing TAIR10 chromosomes. This is incorrect as there is no  
> TAIR10 genome assembly.
>
> Also, I would like to suggest using a different term for the TAIR9  
> assembly in order to avoid future confusion. Please use the term:  
> A_thaliana_Jun_2009. This is what we are using to designate this  
> genome assembly in the Integrated Genome Browser QuickLoad and DAS  
> systems. It would be great if the DAS registry could either  
> recognize this as a synonym for TAIR9 or use this term instead so  
> that people will not continue to be confused about the meaning of  
> TAIR*.
>
> Best wishes,
>
> Ann Loraine
> ____________________
> Ann Loraine
> Associate Professor
> Dept. of Bioinformatics and Genomics, UNCC
> North Carolina Research Campus
> 600 Laureate Way
> Kannapolis, NC 28081
> 704-250-5750
> www.transvar.org
>
>
>
> -----Original Message-----
> From: Jonathan Warren [mailto:jw12 at sanger.ac.uk]
> Sent: Tue 6/28/2011 8:46 AM
> To: gramene at gramene.org
> Subject: Old versions?
>
> Hi
>
> Do you still host old versions of gramene? if so where are they?
> More specifically the DAS sources for say TAIR 9...7etc rather than
> TAIR 10? If they exist I can register them with the DAS Registry and
> they maybe useful for the DAS community and researchers?
>
> Thanks in advance
>
> Jonathan Warren
> Senior Developer and DAS coordinator
> blog: http://biodasman.wordpress.com/
> jw12 at sanger.ac.uk
> Ext: 2314
> Telephone: 01223 492314
>
>
>
>
>
>
>
>
>
> --
>  The Wellcome Trust Sanger Institute is operated by Genome Research
>  Limited, a charity registered in England with number 1021457 and a
>  company registered in England with number 2742969, whose registered
>  office is 215 Euston Road, London, NW1 2BE.
>
>

Jonathan Warren
Senior Developer and DAS coordinator
blog: http://biodasman.wordpress.com/
jw12 at sanger.ac.uk
Ext: 2314
Telephone: 01223 492314










-- 
 The Wellcome Trust Sanger Institute is operated by Genome Research 
 Limited, a charity registered in England with number 1021457 and a 
 company registered in England with number 2742969, whose registered 
 office is 215 Euston Road, London, NW1 2BE. 
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