Ensembl Release 62

We have just updated the Ensembl genome browser and underlying databases to version 62.  We would like to share some new features with our user community.

The new Ensembl release hosts a new species- the white-cheeked gibbon (Nomascus leucogenys).  A new genebuild has been performed using the Ensembl gene annotation pipeline, incorporating both gibbon and human sequences to determine the gibbon gene set.   Compara has also incorporated the gibbon genes and genome into comparative genomics analyses, as is usual for new genebuilds.  Gibbon can now be found in gene trees, a pairwise whole genome alignment with human , and a 35-way multi-species alignment.  View these alignments in views like this one.

BigWig files are now supported through attachment of a url to Ensembl.  Click on ‘Manage your data’ at the left of a location page, and select ‘Attach Remote File’ from the new menu.

Not sure what Ensembl has to offer, or how to use our resources?  Now whenever you search for a term, hits to Help and Documentation will come up.  These may be to page-specific help, FAQs or the glossary, depending on the term.  As always, we hope our users make requests- if you can’t find what you’re looking for, let our helpdesk know.

Finally, SIFT and PolyPhen predictions are available in human variation pages, and in the popular Variant Effect Predictor (for human).  A more detailed post on these variation analyses will be coming soon, so keep your eye on the blog.

More features like the new comparative genomics navigation menu have been released, so explore and let us know what you think.  More news is available on our website.

8 thoughts on “Ensembl Release 62

  1. Hello.

    I’m using your BLAST tool between human and gorilla sequences since a while. I used to get the cDNA sequence of transcripts found in Gorillas.But I have a issue today. When I try to export data from the menu cDNA I only get this :

    ” >10 dna:chromosome chromosome:” and the sequence”coordinates.

    This differ for what I used to get:

    transcript code and “cdna:NOVEL_protein_coding”.

    Did anything change since the last update I am not able to see ?

    Thank you for your good job.

  2. Hello Wilfried,

    It would help if you let me know exactly how you are exporting the data. For example, if I export cDNA sequencing using the ‘Export Data’ link from a gene page, I get what I expect:

    http://www.ensembl.org/Gorilla_gorilla/Gene/Summary?g=ENSGGOG00000007069;r=8:100603605-100605355;t=ENSGGOT00000007097

    Are you exporting from the browser, and if so, how?

    Please send these details to helpdesk@ensembl.org, so we can track it in our system.

    Thanks,
    Giulietta

  3. Hi,

    we incorporate a gene download from you database in our software. Since today it seems that this doesn’t work any longer. The only data our customers and we get is this:

    Location:

    Gene:

    338736

    This is not what we expect.
    What have been done to the database link which worked until yesterday?

    Greetings

    Volker

    • Hi Volker,

      Please report bugs to helpdesk@ensembl.org, so we can track the report.
      We have found a bug in export from the transcript tab, that will be soon fixed. However, I’m not sure exactly what you are doing- can you please email helpdesk with the page/url you are using, and how you are trying the download? This way we can target the exact issue.

      Many thanks.

  4. Wilfried, the export data link should now work from our website.
    Volker, if our fix has not solved your problem, can you give me a bit more detail about how you are downloading Ensembl data?

  5. Greetings,

    I’ve been doing some head to head comparisons between Ensembl release 62 and 60 and have been observing some surprising differences. Could clarify on the below:
    1) Ensembl gene IDs changing location to a different chromosome
    2) Retired genes with mRNA evidence (e.g., ENSMUSG00000057088)
    3) Well established isoforms (maintained for a dozen releases) are now missing (e.g., ENSMUST00000100740).

    The biggest issue for me is number 3. As I heavily rely on alternative isoform information from Ensembl along with associated domain information, it is hard to see why many isoforms are now missing.

    Thanks,
    Nathan

    • Hello Nathan,

      These questions are good ones to send to the helpdesk (helpdesk@ensembl.org).
      We can track the issues in our ticketing system there, and you are guaranteed a fast response.

      To answer, I have asked our mouse genebuilder Amy to comment.

      These issues are a result of the new mouse genebuild that occured in Release 61. For more information about the genebuild look at the document on the mouse homepage.

      http://www.ensembl.org/Mus_musculus/Info/Index

      (the detailed information about genebuild link).

      Response to your questions:

      (1) The gene IDs are assigned automatically by the stableID-mapping
      code. At the moment the code doesn’t penalise assigning stable ID on say
      chromosome 1 from one release to chromosome 6 in the subsequent release.
      We (the genebuilders) are aware of this phenomenon of stableIDs changing
      “location” but we depend on the core team to help us with developing the
      stableID-mapping code, so I’m afraid the issue will remain for the time
      being.

      (2) The example highlighted (ENSMUSG00000057088) contains 1
      transcript (ENSMUST00000014525). In release 62, the gene was not built,
      most likely because the protein supporting evidence (Q8VCX0) was made
      obsolete by Uniprot. Moreover, even if the model had been built in this
      region, it would have been thrown out during production (before the data
      went public) because of the presence of a frameshift intron. See our
      archive page for details.

      We need to investigate question 3 a bit further, and will reply.

      Hope this helps.

      • Thanks for the detailed response. I realize that delving into these issues on a genome-wide basis is complex, however, I appreciate the follow up as these predictions play an important role in the interpretation of a large number of experimental studies.