Trixie the Triceratops

Ensembl produce high quality gene annotation for a number of species, but getting it to the high quality we expect takes time. This means there are many species and strains where we don’t have annotation yet. If you’re working with a species without Ensembl annotation (like Trixie the Triceratops here) or even a specific strain that we don’t have, you can still make use of VEP for predicting the effect of variants on genes and transcripts, using your own annotation. All you need is a GFF or GTF of the transcripts, and a FASTA file of the genome.

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You might know that we offer training courses on using the Ensembl browser, but did you know that we also offer Ensembl REST API and Ensembl Train the Trainer courses? We can come to you to deliver any of these courses at your institute and we don’t charge any fees. If you’re in a low-middle income country, we don’t even charge you for expenses.

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Functional genomics data from DANIO-CODE has been released to the public. This international effort, similar to ENCODE in human and mouse, seeks to characterise the functional elements in the zebrafish (Danio rerio) genome. Announced on Saturday at the International Zebrafish Conference, the DANIO-CODE dataset exists as a track hub, which can be viewed in Ensembl.

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One of the biggest headaches when working with insertions and deletions is how many different ways you can represent the same variant. If you’re looking to find out if there’s already known allele frequencies or phenotypes at a locus, you want to make sure that you find the right one. The VEP can take that headache away through normalisation of variants.

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For the third year in a row, we’re lucky to have student developers working with us as part of Google Summer of Code. We’ve got three GSOC-ers this year, working on some really exciting projects: Zeyu Tony Yang, working on primary genome analysis, Nabil Ibtehaz, working on transcript-level orthology and Somesh Chaturvedi, working on retrieving reference sequences with APIs.

GSOC is a project set up by Google that places students in open source projects to take on a short independent coding project, and pays them for it. We have to pass rigorous selection criteria to be allowed to offer projects on GSOC, and the students have to be selected by both Google and us to take part. It means the GSOC-ers are the Top Gun of student developers. We think this is a really great opportunity, both for open source projects like us, who get a fresh pair of eyes to take a look at something that we’ve maybe put on the back-burner, and for the students, who get experience working on a real-world coding project during their university summer break.

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