Random ramblings about some random stuff, and things; but more stuff than things -- all in a mesmerizing and kaleidoscopic soapbox-like flow of words.
Here is an example success story of using phylogenetic information to improve human gene annotation. What do you see wrong in this EnsemblCompara GeneTree?
The human gene prediction has been split into one third to the left and two thirds to the right. Some of the other species have the full length prediction, but some of the 2x and projected genomes also have this issue. This case was reported to the Havana team at the Sanger and they have now built a human and mouse full-length prediction for the gene (notice the Havana_genes
blue and dark green
The next Ensembl/Havana merge will hopefully reflect this change but, right now, you need to activate the Havana_genes DAS track to see the most up-to-date Havana annotation. There is a good number of these fixed now in the highly loved genomes, aka human, mouse and zebrafish. But there is a second level of genomes that are not getting any manual annotation here but may be annotated somewhere else...
Labels: ensembl, genomics