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Ensembl Tools

We provide a number of ready-made tools for processing both our data (Biomart and the Virtual machine) and yours. For the latter:

  • The VEP processes jobs via a ticketing system and can handle medium to large files (up to 50Mb).
  • For other jobs, only small datasets of up to 5Mb can be uploaded and processed online. We aim to extend the ticketing system used for VEP to these tools.
  • For larger datasets we provide an API script that can be downloaded (you will also need to install our Perl API to use these).
NameDescriptionOnline toolDownload codeDocumentation
Variant Effect Predictor
Analyse your own variants and predict the functional consequences of known and unknown variants via our Variant Effect Predictor (VEP) tool.ToolDownloadDocumentation
BLAST/BLATSearch our genomes for your DNA or protein sequence.ToolDocumentation
BioMartUse this data-mining tool to export custom datasets from Ensembl.ToolDownloadDocumentation
Assembly converterMap (liftover) your data's coordinates to the current assembly.Tool
ID History converterConvert a set of Ensembl IDs from a previous release into their current equivalents.ToolDownload
Ensembl Virtual MachineVirtualBox virtual Machine with Ubuntu desktop and pre-configured with the latest Ensembl API plus Variant Effect Predictor (VEP). NB: download is >1 GB-DownloadDocumentation