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[Bio-software] EvidentialGene improves mRNA-assembly genes above genome-genes for animals and plants

Don Gilbert via bio-soft%40net.bio.net (by gilbertd from net.bio.net)
Wed May 1 10:37:58 EST 2013



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, gilbertd from indiana.edu



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