It’s probably reasonable to assume that the coding sequence (CDS) of a protein-coding transcript model is the feature that is of primary interest to most people who use Ensembl. However, both the 5’ and 3’ untranslated regions (UTRs) are important biological entities in their own right, and it is vital that we in Ensembl do the best we can to represent them accurately. However, the annotation of these UTRs is complicated, so we’re going to focus on exploring the annotation process for 3’ UTRs in this article (Figure 1).

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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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One of the biggest highlights of the new Ensembl Plants release 40 is the inclusion of the new Wheat (RefSeq v1.0) genome from the International Wheat Genome Sequencing Consortium (IWGSC).

The path to sequencing the wheat genome has been no easy ride, due to its large and highly repetitive genome. This new assembly from the IWGSC bridges many gaps from the initial genome sequencing effort. Read on to find out more about this exciting new genome assembly!

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We’ve been tending the Ensembl Plants garden with great care, have cultivated several new species and updated a number of genome assemblies, including a new chromosome-level wheat genome from IWGSC. The protist team have also been busy and are proud to announce an updated assembly for Leishmania major.

Read on to find out more about these exciting new updates and more in this new release of Ensembl Genomes!

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