Author Archives: Fiona, on behalf e! Variation

Comparative Genomics Project Leader

Posted on January 21, 2013 by Fiona, on behalf e! Variation

Are you interested in joining the Ensembl project based in the UK, near Cambridge? The Comparative Genomics team currently has an open position for a Project leader. The Ensembl Compara team develops new and established methods for: whole genome sequence alignment, assignment of … Continue reading →

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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 →

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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 →

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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 →

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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 →

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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 →

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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 →

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SNP consequences

Posted on November 24, 2009 by Fiona, on behalf e! Variation

Did you know that you can use the ensembl API to predict the consequences of your own SNP positions? This is a really popular question and there is some example code on the website to guide you through this. See … Continue reading →

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