Excerpted from the Vega main page:
"The Vertebrate Genome Annotation (VEGA) database is designed to be a central repository for manual annotation of different vertebrate finished genome sequence. In collaboration with the genome sequencing centres Vega attempts to present consistent high-quality curation of the published chromosome sequences."
"Finished genomic sequence is analyzed on a clone by clone basis using a combination of similarity searches against DNA and protein databases as well as a series of ab initio gene predictions (GENSCAN, Fgenes)."
"In addition, comparative analysis using vertebrate datasets such as the Riken mouse cDNAs and Genoscope Tetraodon nigroviridis Ecores (Evolutionary Conserved Regions) are used for novel gene discovery."
NOTE: VEGA annotations appear only on chromosomes 14, 20, and 22 in this assembly.
Thanks to Steve Searle at the Sanger Institute for providing the GTF and FASTA files for the Vega annotations. Vega gene annotations are generated by manual annotation from the following groups:
Chromosome 14:
Genoscope
Relevant publication: Heilig et al., The DNA sequence and analysis of
human chromosome 14. Nature 421:601-607 (2003).
Chromosome 20:
The HAVANA Group,
Wellcome Trust Sanger Institute
Relevant publication: Deloukas et al., The DNA sequence and
comparative analysis of human chromosome 20. Nature 414:865-871 (2001).
Chromosome 22: Chromosome 22 Group,
Wellcome Trust Sanger Institute
Relevant publications:
— Collins et al., Reevaluating Human Gene Annotation:
A Second-Generation Analysis of Chromosome 22. Genome Research 13(1):27-36 (2003).
— Dawson et al., A
first-generation linkage disequilibrium map of
human chromosome 22. Nature 418:544-548 (2002).
— Dunham et al., The DNA sequence of human chromosome 22. Nature 402:489-495 (1999).