EvidentialGene update: Gene-omes from mRNA-seq assembly overtake genome gene-predictions
An existing dogma in genome projects, that quality of a gene set is dependent on the
quality of the genome assembly, is no longer accurate.
mRNA-seq assembly now does as well or better than genome-gene modelling.
Both together, with methods that emphasize mRNA-seq assembly and address
genome-assembly and prediction errors, do the best.
Learn more of this at http://arthropods.eugenes.org/EvidentialGene/
with summary of methods, results in this poster document
http://arthropods.eugenes.org/EvidentialGene/about/EvigeneRNA2013poster.pdf
A recent plant gene set comparison puts Cacao tree genes of the Mars/USDA project,
built with Evigene methods at top for plant gene-set completeness.
For banana, mRNA-only genes are equal to genome-genes.
http://arthropods.eugenes.org/EvidentialGene/plants/
A forecoming killifish gene set using Evigene methods is at top of
10 fish gene sets for completeness, above sets from NCBI and Ensembl
gene modelling methods.
A still-in-progress Daphnia magna gene set is near/at top of arthropod
gene set completeness, and mRNA-only gene assemblies for zebra tick,
a beetle and other arthropods are good shows versus genome-gene sets.
The Evigene mRNA-assembly pipeline software is working well enough in
other people's hands now, and they are finding same sorts of results
that I find:
http://www.slideshare.net/AustralianBioinformatics/combining-transcriptome-assemblies-kenleenakasugi
using this
http://arthropods.eugenes.org/EvidentialGene/about/EvidentialGene_trassembly_pipe.html
-- Don Gilbert
