[ensembl-dev] Ensembl 96 and Ensembl Genomes 43 are out!

[Carla Cummins]

Hi Malcolm,

Thank you for your question. I don't believe that there was an 
announcement regarding this alignment. Every time some new eligible 
species are included in Ensembl, they are automatically added to the 
relevant MSA. We consider this "business as usual" and do not tend to 
make announcements about it. Apologies.

Regarding your other questions, the 25 fish alignment replaces an MSA 
with fewer fish species - previously 23. The current assembly of Mexican 
tetra has been a part of Ensembl - and therefore our alignments - since 
release 94 (Oct 2018). However, it was previously referred to as 'Cave 
fish' rather than 'Mexican tetra', which is probably a little confusing. 
Prior to release 94, we had an earlier assembly, which has been present 
since late 2013. Below are some links to statistics on these fish 
alignments for the previous few releases, to show the progression of 
this MSA:

http://www.ensembl.org/info/genome/compara/mlss.html?mlss=1497

http://jan2019.archive.ensembl.org/info/genome/compara/mlss.html?mlss=1371

http://oct2018.archive.ensembl.org/info/genome/compara/mlss.html?mlss=1332

http://jul2018.archive.ensembl.org/info/genome/compara/mlss.html?mlss=1133

I hope this helps,

Carla

---
Dr Carla Cummins
Ensembl Compara Developer
EMBL-EBI, Wellcome Genome Campus
Hinxton, Cambridge
CB10 1SD
United Kingdom


On 21/05/2019 16:26, Cook, Malcolm wrote:
>
> Hello,
>
> I read at 25 fish EPO 
> <https://www.ensembl.org/info/genome/compara/mlss.html?mlss=1497> that 
> “This alignment has been generated in Ensembl release 96”
>
> Yet I see no mention of it in Ensembl 96 and Ensembl Genomes 43 are 
> out! 
> <http://www.ensembl.info/2019/04/09/ensembl-96-and-ensembl-genomes-43-are-out/>
>
> Is this perhaps:
>
>  1. an oversight on your part
>  2. or might the fish alignment be older that this
>  3. or I should expect to find announcements re comparative genomics
>     efforts elsewhere?
>  4. Or am I otherwise misunderstanding how Ensembl is organized.
>
> Also, is there anywhere an announcement for the alignment I might 
> share among possibly interested colleagues,  and is there anywhere a 
> description of what it is replacing (if anything) (esp: was there a 
> prior fish MSA that included Mexican tetra?),
>
> Thanks very much,
>
> ~Malcolm Cook
>
> *From:*Dev <dev-bounces at ensembl.org> *On Behalf Of *Astrid Gall
> *Sent:* Tuesday, April 9, 2019 7:01 AM
> *To:* dev at ensembl.org; announce at ensembl.org; ensembl-campus at ebi.ac.uk
> *Subject:* [ensembl-dev] Ensembl 96 and Ensembl Genomes 43 are out!
>
> **CAUTION: Non-Stowers email**
>
> Dear all
>
> We are pleased to announce that the latest Ensembl and Ensembl Genomes 
> updates have been released:
>
> http://www.ensembl.org/
>
> http://ensemblgenomes.org <http://ensemblgenomes.org/>
>
> Highlights of this release include:
>
>   * First-pass full annotation of the mouse genome (GENCODE M21 gene set)
>   * Release of Ensembl-RefSeq MANE Select v0.5 transcripts
>   * Update to GENCODE 30 for human
>   * Joint REST server for Ensembl and Ensembl Genomes
>   * Changes to FTP directory layout
>   * New genomes: 19 birds, five reptiles and 12 mammals
>   * New interface for configuration of regulation tracks
>
> The release blog post with all news can be viewed here:
>
> http://www.ensembl.info/2019/04/09/ensembl-96-and-ensembl-genomes-43-are-out/
>
> For the latest news from the Ensembl project visit our blog at:
>
> http://www.ensembl.info <http://www.ensembl.info/>
>
> The release webinar is planned for Wednesday 17th April 2019 at 16:00 
> BST. Please register using the following URL:
>
> https://attendee.gototraining.com/r/8260823671959775489
>
> Registration is free.
>
> Best regards,
>
> Astrid
>
> On behalf of the Ensembl team
>
> --
>
> Dr Astrid Gall
>
> Ensembl Outreach Officer
>
> European Molecular Biology Laboratory - European Bioinformatics 
> Institute (EMBL-EBI)
>
> Wellcome Genome Campus
>
> Hinxton, Cambridge
>
> CB10 1SD
>
> United Kingdom
>
>
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-- 
Carla Cummins, Ph.D.
Ensembl Compara Developer
European Bioinformatics Institute (EMBL-EBI),
European Molecular Biology Laboratory,
Wellcome Trust Genome Campus, Hinxton,
Cambridge, CB10 1SD, United Kingdom
Room A3-145
Phone + 44 (0) 1223 49 4240
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