nsSNP annotations

Introduction

Each non-sysnonymous coding snp within Ensembl is predicted to be either potentially 'neutral' or 'disease' associated with a confidence score. These predictions were made using the J48 decision tree classifier and annotated VARIANTS in SWISSPROT as a training dataset [1]. Ensembl allows us to attach these functional predictions as a DAS annotation to Ensembl genome browser displays.

Perform the following steps to attach these predictions to the Ensembl genome browser display.

Configuration

  • Add custom data - Within the Human genome browser click 'Add custom data to page' in the left navigation menu.

  • Attach DAS - Click the 'Attach DAS' link on the left of the configuration window.

    • Enter the URL http://www.brightstudy.ac.uk/cgi-bin4/das within the DAS server text box.

    • Select 'snp_das' from the list of returned DAS sources.

    • Click next. Tick 'Chromosome NCBI35', click next, then close the window and that's it.

Reference