We are updating SIFT and PolyPhen-2 predictions of missense variant deleteriousness in the Ensembl browser and Ensembl VEP with the new release 109. We have recalculated all scores using newer software versions, updating PolyPhen-2 from 2.2.2 to 2.2.3 and SIFT from version 5.2.2 to 6.2.1. When we update software and reference data versions, we expect to see changes in some predictions. This is a guide as to what you can expect.
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Cool stuff Ensembl VEP can do: display variants on AlphaFold-predicted 3D protein structures
The AlphaFold AI system developed by DeepMind predicts a protein’s 3D structure from its amino acid sequence. You can now view variant locations on AlphaFold predicted structures in the Ensembl VEP web tool.
Continue readingCool stuff Ensembl VEP can do – provide evidence of protein interaction impact
Ensembl VEP integrates information from many different resources to help you interpret the functional impact of your variants. It now reports when variants fall in sites with evidence of impact on protein interactions, as described in the IntAct database.
Continue readingCool stuff Ensembl VEP can do: run faster with Nextflow
Ensembl VEP is now wrapped in a Nextflow pipeline which means you can analyse large variant sets more quickly using simple parallelisation.
Continue readingCool stuff Ensembl VEP can do: flagging variants predicted to allow NMD escape
A new plugin was released in Ensembl VEP version 105 which reports when a variant introducing a premature stop codon may allow the transcript to escape nonsense-mediated decay (NMD).
Continue readingUpdated G2P terms supported in Ensembl VEP
Recent changes to the terms used in the G2P database are aligned with global standards, but are not compatible with old versions of the VEP G2P plugin. We’ve updated the latest version of the VEP G2P plugin (Ensembl 105) to be compatible with both the old and new formats.
Continue readingCool stuff Ensembl VEP can do: protein annotations from neXtProt
Together with the neXtProt team, we’ve created a plugin for the command-line VEP tool to retrieve and report information about the protein location of missense and stop gained variants.
Continue readingUsing Ensembl VEP with Windows 10
Ensembl VEP has been developed for use on Linux systems and we recommend installing on a Linux system for the optimal installation and usage experience. However, we occasionally receive queries about using VEP in the Windows environment – this guide will help you get going if you are using Windows 10.
Continue readingCool stuff the VEP can do: Singularity
The quickest and most flexible way to run Ensembl VEP on large scale variant sets is to install and run it locally. Depending on the use case, the underlying architecture, and the available permissions, installing VEP prerequisites is prone to complications. To aid with this, we have made the VEP available with containers.
Continue readingCool stuff Ensembl VEP can do: disease information from DisGeNET
To better understand how your variants might be linked to disease, you can add information from DisGeNET to your VEP analysis. DisGeNET integrates data from expert curated repositories, GWAS catalogues, animal models and the scientific literature, to provide disease associations with genes and variants.
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