[ensembl-dev] Ensembl release 72 is out!

[Hiram Clawson]

Good Afternoon Thibaut:

Yes, I saw the updates to the chrMT sequences.

I'm also seeing differences in other genes on the assemblies.
In come cases just a few genes, but at least a few genes in
every single assembly.  For example, in one of the assemblies with only
a few gene differences, the difference between:
   Drosophila_melanogaster.BDGP5.71.gtf.gz
   Drosophila_melanogaster.BDGP5.72.gtf.gz
37 gene difference:
FBtr0075203 FBtr0078307 FBtr0081127 FBtr0089441 FBtr0089442 FBtr0089481
FBtr0100471 FBtr0100472 FBtr0100577 FBtr0100578 FBtr0100579 FBtr0100580
FBtr0100581 FBtr0100582 FBtr0305796 FBtr0308123 FBtr0308208 FBtr0308209
FBtr0330269 FBtr0330270 FBtr0330271 FBtr0330272 FBtr0330273 FBtr0330274
FBtr0330275 FBtr0330276 FBtr0330277 FBtr0330278 FBtr0330279 FBtr0330280
FBtr0331503 FBtr0331504 FBtr0332570 FBtr0332571 FBtr0332976 FBtr0332977
FBtr0332978

The GTF files appear to have an extra exon definition.  A higher
count difference, for example in:
  Loxodonta_africana.loxAfr3.71.gtf.gz
  Loxodonta_africana.loxAfr3.72.gtf.gz
has 644 different gene predictions.

The largest difference is in one of the smallest genomes:
    Takifugu_rubripes.FUGU4.71.gtf.gz
    Takifugu_rubripes.FUGU4.72.gtf.gz
with 2004 different gene predictions.  For example,
ENSTRUG00000004473 now has a start codon in version 72 where
it did not before.  Perhaps the difference is an improvement.
scaffold_20     protein_coding  start_codon     157857  157859

Is it known if the prediction pipeline has had something fixed to
improve these gene definitions ?

--Hiram

On 6/25/13 3:05 AM, Thibaut Hourlier wrote:
> Hi Hiram,
> We have added mitochondrion to several species which means that we have added 37 genes and the mitochondrial sequence. Therefore we had to update the genebuild.last_geneset_update meta_key.
> Here are the species:
> 	• Alpaca
> 	• C.savignyi
> 	• Dolphin
> 	• Hedgehog
> 	• Hyrax
> 	• Lamprey
> 	• Lesser hedgehog tenrec
> 	• Medaka
> 	• Pika
> 	• Platyfish
> 	• Tarsier
> 	• Tree Shrew
> 	• Xenopus
>
> Hope this helps
> Thibaut
>
> On 24 Jun 2013, at 17:53, Hiram Clawson <hiram at soe.ucsc.edu> wrote:
>
>> Good Morning EnsGene Fans:
>>
>> I'm noting an unusual characteristic of this release compared to previous
>> releases.  Normally, a new release has several assemblies that have updated
>> their gene predictions.  Many assembly gene predictions remain the same
>> from one release to the next.
>>
>> In this release 72 I'm seeing all assemblies have updated at least
>> some gene predictions.  I'm wondering if maybe my tools here have
>> broken or changed, or is this actually true that I would find at
>> least some gene predictions in each assembly have changed in this release ?
>>
>> --Hiram
>>
>> On 6/19/13 6:06 AM, Rhoda Kinsella wrote:
>>> We are pleased to announce that the latest Ensembl update (e!72) has been released : http://www.ensembl.org/
>>>
>>> Highlights of this release include:
>>>
>>> Human:
>>> Updated patches for the human assembly (GRCh37.p11)
>>> Updated HAVANA manual curation for human
>>>
>>> Other species:
>>> Updated HAVANA manual curation for mouse
>>> Updated mitochondrial sequence and annotation for several species including alpaca, lamprey, platyfish and xenopus.
>>>
>>>
>>> Other news:
>>> New variation citation page and individual genotype search box
>>> We have added the ability to upload a VEP output file to the website
>>>
>>> A complete list of the changes in release 72 can be found at http://www.ensembl.org/info/website/news.html
>>>
>>> For the latest news from the Ensembl project visit our blog at http://www.ensembl.info
>>>
>>> The release blog post can be viewed here: http://www.ensembl.info/blog/2013/06/19/ensembl-72-has-been-released/
>>>
>>>
>>> Best Regards,
>>> Rhoda
>>>
>>>
>>> Rhoda Kinsella Ph.D.
>>> Ensembl Production Project Leader,
>>> European Bioinformatics Institute (EMBL-EBI),
>>> Wellcome Trust Genome Campus,
>>> Hinxton,
>>> Cambridge,
>>> CB10 1SD
>>
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