Ensembl tools

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Click the tools button at the top of the browser to reveal some useful programs. 

Each tool has an online interface and an API script to be used in conjunction with the Ensembl Perl API.

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The Variation Effect Predictoris our most popular tool. Enter in transcript or genomic coordinates to determine the effect of sequence variation on transcripts and proteins. A dbSNP identifier will be given in the output, if there is a matching one.

Region Report accepts genomic coordinates, and outputs genes, sequence, variants, and other data in that region. The output is customisable.

The Assembly Converter allows coordinates from an older genome sequence to be updated to new coordinates (and vice-versa). As genomes are sequenced, the improved technology allows current genome sequence to be more accurate, containing fewer gaps and fewer mistakes. Using the most recent genome version or assembly is advised. Ensembl, the UCSC genome browser, and NCBI Map Viewer strive to show all annotation on the newest assembly possible, once the genome sequence is released to the public.

Virtual Machine A VirtualBox virtual Machine is available, with a Ubuntu desktop and pre-configured with the latest Ensembl API plus Variant Effect Predictor (VEP).

ID History converter displays IDs that are in the current version of Ensembl. Start with a list of old IDs, and see which ones are still used, and which ones have been ‘retired’, or changed into a different ID. Though Ensembl IDs are stable (a gene or transcript should always have the same ID), the ID can change if one gene is split into two, or two genes that were erroneously split in a previous release are fused together into one.

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Archive sites let you view past versions of Ensembl, including older gene sets.