If a variant hits a splice site, you want to know if splicing is going to occur as normal, or if you can expect a different protein isoform. We have a few cool tools with the VEP that will help you to assess that for your own variants.
In this blog we catch up with Ensembl’s 2018 Google Summer of Code (GSoC) students and hear about their now completed projects, and their reflections on the experience. You may have already seen our previous blog post which we published as they were just beginning their projects. Read on to find out how they went, what they learnt and what valuable advice they can pass on to aspiring GSoC students.
We’ve heard from a number of you about missing paralogues in release 94. We have lost some paralogy relationships and we’re looking to restore them in future. We’re sorry for any problems this caused.
If you work with Zymoseptoria tritici genes, we’re looking for your help. We need people to get involved with community annotation of genes.
In its latest release, Ensembl has completely reviewed its reporting of potential Transcription Factor (TF) binding sites. TF proteins are key players of gene expression regulation that bind to specific DNA regions characterised by approximate sequence patterns, or transcription factor binding motifs (TFBM). These motifs are generally represented as a Position Specific Frequency Matrix, or Binding Matrix. Ensembl scans genomes for occurrences of these motifs, reporting Motif Features at each possible location.
This blog post is a joint contribution by Joannella Morales, Jane Loveland, Adam Frankish, Fiona Cunningham and Astrid Gall.
We are pleased to introduce the Matched Annotation from the NCBI and EMBL-EBI (MANE) project. This new joint initiative between EMBL-EBI’s Ensembl project and NCBI’s RefSeq project aims to release a genome-wide transcript set that contains one well-supported transcript per protein-coding locus. All transcripts in the MANE set will perfectly align to GRCh38 and will represent 100% identity (5’UTR, coding sequence, 3’UTR) between the RefSeq (NM) and corresponding Ensembl (ENST) transcript.
We’ve just released Ensembl Genomes 94, which includes genomes for Emmer wheat and over 200 new fungi, updated gene trees and host-pathogen interactions from PHI-base.
The latest version of Ensembl, release 94, is out and have we got some treats for you. As well as GENCODE updates for human and mouse, we’ve also got loads of new fish. Plus, we have brand new transcription factor binding motifs, additional predictors of variant pathogenicity and updated gene tree pipelines.
A common use case for the VEP is as a first step towards identifying the causal genetic variant of a rare phenotype from whole genome/exome sequencing. The VEP tells you which genes are hit, what effects they have on them, and you have to begin the long laborious process of filtering those down. Things you might consider include allele frequency, association with genes known to be involved in rare disease and whether both genes in a diploid organism are affected. Rather than faffing about doing this manually, you can use the G2P (genotype to phenotype) plugin instead, which was recently published as a preprint.