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[Bio-software] EvidentialGene genomics software update, 2016 Feb

Don Gilbert via bio-soft%40net.bio.net (by gilbertd from net.bio.net)
Mon Feb 22 22:14:56 EST 2016



Dear genomics folks,

Re: EvidentialGene project at  http://eugenes.org/EvidentialGene/

EvidentialGene has a high accuracy rate for gene set construction, compared
with other gene informatics methods, for fish, plants, various arthropods.
Recently I've generated gene sets for two Anopheles mosquito species with
Evigene mRNA assembly, and they surpass recently published gene sets from
Vectorbase project in orthology completeness. Improvements to the gene locus
classifier, including chromosome-assembly map classifier, are producing better
discrimination of alternate transcripts versus paralog genes.

I hope to offer an update in coming months that (a) improves gene locus
classification (removing some duplication, improving alternate transcript
classification), and (b) offering an initial mRNA-assembly by chromosome
assembly classifier (i.e. genome mapping of transcript assemblies).  

If you have interests in accurate animal and plant gene-ome construction from
RNA sequences, with or without a chromosome assembly, this project may be of
interest. I would like to work with a few collaborators who have genome +
transcriptome data sets plus genome-modelled gene sets (e.g. from pipelines
such as MAKER, NCBI, Augustus, EvidenceModeller, etc) to compare with
EvidentialGene results.

The software pipeline pair of MAKER+Trinity form a common recipe now for
genome biologists, without those scientists realizing that greater accuracy is
possible and not too much harder to obtain, I suspect.

For quality effect of gene set construction methods for vertebrate fish,
comparing methods NCBI Eukaryote annotation (nc), EvidentialGene (evg), MAKER2
(mk), EvidenceModeller (em), within and across species, see
http://eugenes.org/EvidentialGene/vertebrates/


-- Don Gilbert



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