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[Bio-software] EvidentialGene update: Gene-omes from mRNA-seq assembly overtake genome gene-predictions

Don Gilbert via bio-soft%40net.bio.net (by gilbertd from net.bio.net)
Sat Feb 8 07:43:35 EST 2014



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 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 others are good shows versus arthropod 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



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