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[Arthropod] Accuracy of EvidentialGene methods for arthropod gene sets

Don Gilbert via arthropod%40net.bio.net (by gilbertd from net.bio.net)
Fri Nov 28 12:51:39 EST 2014

Dear Arthropod scientists,

When you read new arthropod genome papers, do you wonder how accurate
the biological and phylogenetic interpretations of genes and genomes
are?  Many animal/plant genome papers today are using genome informatics
methods that are not as accurate as they can be.  Some interpretations
of gene losses, gains, and gene qualities may be attributed to artifacts
of methods, but how do you distinguish artifact from biology?

The gene construction methods called EvidentialGene that I've work out
over several years now are at the point of producing highly accurate
gene sets, when measured with objective biological criteria of orthology
completeness, that is, the presence and fullness of protein coding genes
that share orthology with related species.  See this recent summary at

"EvidentialGene sets are Best of clade in gene set completeness  
for 11 species of Arthropods, Plants and Fishes. " [link]

This interpretation that I believe others can reproduce, is that
EvidentialGene methods are producing the most accurate gene sets
for these arthropods, plants and other animals.

These are in comparison to other good and widely used gene prediction/production
methods, including those of current NCBI Eukaryotic Genome Annotation
Pipeline, ENSEMBL's genome annotation pipeline, various genome projects
using Maker, GLEAN, EvidenceModeller, etc + gene predictions.

EvidentialGene methods for mRNA-assembly also are orthology-blind, that is
other species genes are not used in assembling a new gene set, just
in evaluating, so that (a) Evigene sets are also expected to be 
complete for novel or species-unique genes, and (b) artifacts in other 
species gene sets (and in genomes, predictors) are not transferred.

If you are involved in or in contact with projects to produce arthropod
or other animal/plant gene sets, genome- and/or transcriptome-based,
using EvidentialGene methods will improve the biological accuracy of
genes discovered, often by significant amounts.

- Don Gilbert, gilbertd at indiana edu

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