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

[Loraine, Ann]

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









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