EvidentialGene improves mRNA-assembly genes above genome-genes for animals and plants

[Don Gilbert]

Dear bioinformaticians,

If you are working on new genomes and/or transcriptomes for any interesting animal/plant,
you will likely benefit from this improved EvidentialGene work.
The working title of its paper is

Gene-omes without genomes: mRNA sequence assemblies surpass genome models
for accuracy of Animal and Plant genes.

And that is what I find, with results documented below. Constructing good quality genes
from mRNA-seq is now an engineering task, amenable to solving for accurate results.
But there is a trick answer to this that not many others know of yet, as well as
need for good data and effort.

See here
http://arthropods.eugenes.org/EvidentialGene/ especially
http://arthropods.eugenes.org/EvidentialGene/about/EvidentialGene_quality.html
with summaries for animal and plant, mostly arthropod, gene-omes. And see
http://arthropods.eugenes.org/EvidentialGene/about/EvidentialGene_trassembly_pipe.html
for a now somewhat easy to use mRNA-gene processing pipeline that will I hope
provide others the same high quality results.

Among arthropods,
- Pogonus beetle mRNA-genes are more complete than
Tribolium or pine beetle genome genes;
- Zebra tick mRNA-genes are more complete than either
spider mite or Ixodes tick genome-genes;
- for Crustacea, Daphnia magna mRNA-genes are better than
Daphnia pulex genome genes, and Penaeus tiger shrimp mRNA-genes
are about as complete as Daphnia pulex.

Please contact me with questions or comments.

- Don Gilbert, gilb...@indiana.edu