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How does Vega differ from Ensembl ?

  • Whereas Ensembl shows deep datasets (for example Variations and Regulatory Feature Predictions) and computationally derived gene predictions on a large number of whole genomes, Vega shows gene annotations arising from the labour intensive process of manual curation. This approach was applied to the whole of the human, mouse and zebrafish genomes. In addition, small regions of particular biological interest, for example the MHC regions of the gorilla, wallaby, pig and dog genomes have also been annotated.
  • Vega contains annotation of the human LRC region in nine haplotypes and the mouse Insulin Dependent Diabetes (Idd) regions on non-reference assemblies that are not present in Ensembl.

  • For each release of human, mouse and zebrafish, the Havana annotation was projected onto the standard reference assembly. This projection allowed the Vega annotation to be included in Ensembl, both as distinct genes and also as part of the merged Ensembl geneset.
    • Transcripts with a biotype of 'Artifact' were not transferred.
    • Links between the stable IDs of the merged Ensembl and the source Vega genes/transcripts are shown in the 'Alternative genes/transcripts' section of Gene and Transcript Summary Pages.
  • The Vega comparative analysis allows direct comparison of regions in the same species, for example the MHC region in different human haplotypes. This self-comparison is not present in Ensembl.
  • Many Ensembl features are not available in Vega. From the users point of view perhaps the most significant of these is BioMart. However due to their inclusion in Ensembl, Vega human, mouse, zebrafish, rat and pig data can be queried using Ensembl BioMart.