Category Archives: Variation

What’s new for the VEP

Posted on April 24, 2013 by Will (Variation)

It has been quite a while since we’ve blogged about the VEP (Variant Effect Predictor), and in that time we’ve added a whole load of new features, particularly to the downloadable script version. Structural variants The VEP now supports finding … Continue reading →

Posted in Variation | Tagged | 1 Comment

Variants in regulatory regions

Posted on January 24, 2013 by Anja (Variation)

From release 70 we store and display information on the type of consequence a variant has on overlapping regulatory regions (Ensembl regulatory features and Ensembl motif features) for human and mouse. Web display One of the major benefits of this is that we … Continue reading →

Posted in API and schemas, Regulation, Variation | Leave a comment

Variation consequences

Posted on August 6, 2012 by Fiona, on behalf e! Variation

From release 68, we are using Sequence Ontology (SO) terms for the variation consequences, in an effort to standardise terms across the different browsers, making it easier for users to do a cross comparison of variation annotation.  The UCSC Genome Browser … Continue reading →

Posted in Uncategorized, Variation | 1 Comment

SIFT and PolyPhen predictions for human Ensembl and RefSeq proteins

Posted on May 25, 2012 by Fiona, on behalf e! Variation

For release 67 we changed how we store the protein function predictions from SIFT and PolyPhen so that they also can be used for more than just Ensembl transcripts, including RefSeq transcripts. We use these tools to compute the predicted effect of every … Continue reading →

Posted in Uncategorized, Variation | 2 Comments

Importing VCF files

Posted on May 14, 2012 by Will (Variation)

Variant Call Format (VCF) has become the standard portable data format for variation data. Ensembl provides various tools for handling VCF files, such as the ability to upload and view VCF data on the genome browser, and the Variant Effect … Continue reading →

Posted in API and schemas, Variation | Leave a comment

New features in the Variant Effect Predictor

Posted on July 7, 2011 by Will (Variation)

The Variant Effect Predictor (VEP) software can predict the consequence of genomic variants using the genomic annotations provided by Ensembl. In release 63 of Ensembl we have added new features to both the script and web versions of the VEP. … Continue reading →

Posted in Variation | Leave a comment

Come and work in Ensembl!

Posted on June 28, 2011 by Fiona, on behalf e! Variation

If you are a bioinformatician and interested in joining Ensembl at the EBI, the variation team currently has an open position for a software developer. Duties include improving and extending the variation pipelines and API, developing the database schema, integrating … Continue reading →

Posted in Jobs, Uncategorized, Variation | Leave a comment

Variation consequences in release 62

Posted on April 19, 2011 by Fiona, on behalf e! Variation

Variation consequence types, such as “intronic” or “non-synonymous”, describe the variation location or effect of a variation on a transcript. For the latest version of Ensembl (release 62) we have made some significant changes to the way in which we … Continue reading →

Posted in Ensembl, Variation | 3 Comments

SNPs in high LD

Posted on June 11, 2010 by Fiona, on behalf e! Variation

A new section has been added to the variation page in Ensembl 58 that allows you to find other variations in strong linkage disequilibrium with the SNP you are viewing. Clicking on “Linked variations” from the menu on the left … Continue reading →

Posted in Variation | Tagged | 3 Comments

SNPedia in Ensembl

Posted on May 6, 2010 by Fiona, on behalf e! Variation

Ensembl is always extending the variation pages to include more information. Did you know that the latest data from SNPedia is now available? SNPedia is a wiki-style resource for human genetics with public annotation of over 11,000 SNPs, released under … Continue reading →

Posted in Variation | Leave a comment