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 were also annotated.
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.
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
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.