[ensembl-dev] Ensembl release 67 is out!

[Beat Wolf]

Thank you, i was starting to think i was doing something wrong. I hope it can 
be fixed soon. Currently i'm using the archive of biomart, but the server seems 
very unstable and i get many connection problems.

Regards

Beat


On Tuesday 22 May 2012 11.38:27 Rhoda Kinsella wrote:

Hi Beat
We are currently looking into why this has occurred but it is certainly a bug 
in our mart databases. I will respond as soon as we have a fix in place. Thank 
you for reporting this and apologies for any inconvenience.
Regards
Rhoda


On 19 May 2012, at 15:55, Beat Wolf wrote:

Hi,
 
i'm a computer scientist and not a biologist, so perhaps i missed something 
about the DMD gene changing recently.
I have an automated unit test for my application that uses biomart. It happens 
to test the DMD-001 transcript of the DMD gene.
In the 66 version of enembl, the UTR3 coordinates of the exon number 79 where:
 
31137345
to 31140035

which was correct. Now with the version 67 of ensembl, the UTR3 region in the 
same exon is:
 
31137345 to
31137344

Which can not be correct, because that means that UTR3 has a length of 1. The 
other numbers don't match up either.
 
Did the DMD gene change? Is the information stored differently in ensembl? What 
values do i need to reconstruct the true UTR3 region? Or is this a bug in the 
new ensembl version. If yes, how many other genes are affected? Currently i 
will stay on the 66 version thanks to the archives, but i have some connection 
issues with it, it seems to be much less stable than the 67 version.
 
Greetings
 
Beat Wolf
 
On Thursday 10 May 2012 10:58:58 Thomas Maurel wrote:

The latest Ensembl update (e!67) has been released : http://www.ensembl.org/

Here are some highlights:

Human: The patches for the human genome assembly have been updated to 
GRCh37.p7, Human somatic variants from COSMIC have been updated to release 58 
and we now provide the 1000 genomes phase 1 genotype data.

New species:  Nile tilapia (Oreochromis niloticus).

New genomes: The assemblies for Pig and Squirrel have been updated.

A complete list of the changes in release 67 can be found 
at http://www.ensembl.org/info/website/news.html

For the latest news on the ensembl project visit our blog 
at http://www.ensembl.info/



The release blog post can be viewed here 
: http://www.ensembl.info/blog/2012/05/10/ensembl-67-has-been-released/


Best regards,
Thomas Maurel


--
Thomas Maurel
Bioinformatician - Ensembl Production Team
European Bioinformatics Institute (EMBL-EBI)
Wellcome Trust Genome Campus, Hinxton
Cambridge - CB10 1SD - UK





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Rhoda Kinsella Ph.D.
Ensembl Production Project Leader,
European Bioinformatics Institute (EMBL-EBI),
Wellcome Trust Genome Campus, 
Hinxton
Cambridge CB10 1SD,
UK.




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