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Ensembl Genomes launches Protists, Bacteria and Metazoa

Bogdan — Tue, 21 Apr 2009 13:27:40 +0000

The following sites are available:

http://bacteria.ensembl.org
http://protists.ensembl.org
http://metazoa.ensembl.org

During summer, two more sites – for Fungi and Plants – should be made available.

Learn more about Ensembl Genomes project.

Ensembl release 51 is out!

Bogdan — Thu, 20 Nov 2008 13:51:34 +0000

This in itself wouldn’t be so exciting, if it were not for the new webcode! If you do visit Ensembl now, you will be definitely surprised with the page loading speed – it is amazingly faster than it used to be! Also, as you dig deeper and deeper, you’ll see that there are a lot more other differences – starting with the new design, and not forgetting the changed page organization logic.

To cut the long story short, here’s the list of changes in the new Ensembl 51 webcode release. Other changes to Ensembl in release 51 are also available.

One of the new features which caught my attention is the ability to add custom tracks in Ensembl (which is a long-available feature in UCSC Genome Browser). Interestingly, you do not even have to be logged in to use this feature. We shall be considering providing the TFBS custom track for several species, as predicted de-novo by our evolutionary conserved tfbs search tool (binding site finder), but this is a long shot, given the already published COTRASIF development roadmap.

There is one more great news which is kinda insufficiently highlighted: the brand-new Ensembl Genome Browser website, which (as planned, it hasn’t yet started operations) will provide access not only to vertebrates, but also to other taxonomy groups. The full list is:

Metazoa
Protists
Bacteria
Plants
Fungi

Weird orthology species names in Ensembl

Bogdan — Tue, 30 Sep 2008 11:01:59 +0000

For the COTRASIF tool, I’ve been using the Ensembl Compara database (since release 47) to automatically import into COTRASIF gene orthology mappings.

However, with the E!50 release, the Compara database was dropped.

Looking for another option to get orthologs from Ensembl (using martservice, via biomart.org), I tried using the standard query – selecting “Homologs” group on the “Attributes” page for a single species database, and then selecting appropriate second species to get orthology mappings.

Imagine my surprise, when not only in the interface, but also in the generated XML file I found attribute names like “cow_ensembl_gene” :-O

I only need 11 species at the moment, and excluding the sufficiently unique name mappings like “zebrafish – danio rerio”, there is a number of questionable mappings: “yeast” for S. cerevisiae (could be S.pombe), “rat” for R. norvegicus (could be R.rattus), “anopheles” for A.gambiae (could be some other Anopheles). Other mappings might be also non-unique, especially for people working with different species of the same genus.

Am I missing some system in this naming “convention”, or am I the only one who finds it strange?

Is there a way not to use “common species names” when importing orthology data from Ensembl with the help of martservice?