I would like to get all human exons from Biomart. It's easy enough to download all exons from Ensembl with their Ensembl IDs, and to download all exons from Vega with their Vega IDs. I figured I would just loop through the files, taking a Vega sequence if it exists, otherwise using the corresponding Ensembl sequence.
The problem is finding the corresponding sequences. I don't know how to translate Ensembl gene IDs to Vega gene IDs. I also can't seem to find another ID that's common to the two systems. EntrezgeneID and Refseq DNA ID, for example, only apply to a subset of the exons. So, is there a web, Perl, or database way to get a list of translations of Ensembl ID to Vega ID, or translations from each of them to some third ID? Or has someone made such a file that I could download? (I didn't find it on the Vega site.) Thanks, - Amir Karger Research Computing Life Sciences Division Harvard University
