FTP downloading and exporting Vega data

Although the Vega databases and API are not publicly available in quite the same way as are the Ensembl resources, the data can still be queried in a variety of ways.

• Sequences and features on regions upto 20Mb in length can be exported in a variety of formats such as FASTA Genbank, etc.

• Larger amounts of data can be downloaded from the Ensmebl FTP site. This contains FASTA files of the assembly, cDNAs and peptides for each Vega species, dumps of the annotation in GTF format, etc.

• Regular datafreezes of Vega human and mouse data included in Ensembl. These can be accessed in a variety of ways:

  • Ensembl MartView allows export of filtered data sets for human and mouse Vega genes.
  • The Ensembl FTP site contains MySQL dumps containing the majority of the Vega annotation (projected on standard assemblies such as GRCh37). These can be can be downloaded, installed locally, and queried using either MySQL or the Ensembl API.
  • Alternatively downloading of the files can be avoided by directly querying the publicly available Ensembl MySQL server.

The differences in genome assemblies between Vega and Ensembl should be considered when interpreting the results of any analysis of data downloaded from Ensembl with that downloaded from Vega.