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EvidentialGene : Evidence Directed Gene Prediction for Eukaryotes

    2014 Feb. news: Evigene sets for Cacao and Killifish are Best of clade for gene set completeness (size, orthology) for plants and fishes.
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2013 Poster : Gene-omes built from mRNA-seq not genome DNA

Independent comparison of EvidentialGene_trassembly doi: 10.1371/journal.pone.0091776

2012 Poster : Perfect Genes Constructed with Gigabases of RNA

EvidentialGene mRNA Transcript Assembly Software 2013 April

EvidentialGene Animal & Plant Genes Quality Comparison

EvidentialGene :
Evidence Directed Gene Prediction for Eukaryotes

  Don Gilbert, gilbertd at indiana edu, 2010 .. 2013

Annotation summary

Informant evidence for gene models is transcript and protein
data.  Transcripts from long (e.g. dbEST) and short reads (e.g.
Illumina), are mapped to the genome assembly with GMAP (long) 
or GSNAP (short).

EST assemblies are constructed using PASA, from all transcript
data.  RNA-seq assemblies are first constructed from aligned short
reads with Cufflinks, and combined with EST reads for a full 

Protein genes from related sequenced genomes are BLASTX aligned to
repeat/transposon-soft-masked genome, then refined with Exonerate to 
protein gene models.

Gene models are predicted with evidence-directed AUGUSTUS
predictor. Augustus is trained for gene parameters
using full cDNA genes derirved from the PASA EST assemblies.

Several prediction sets from different evidence sets and
parameters are combined, selecting highest evidence scored model
per locus, and avoiding artifactual gene splits and joins.  
This consensus gene set has the best match to EST and protein 

Predicted genes are UTR-extended and/or improved by PASA. Genes
are annotated with Uniprot descriptions, and classified by
evidence scores including transposable elements.

Software references:
  AUGUSTUS: http://augustus.gobics.de/
  GMAP-GSNAP: http://research-pub.gene.com/gmap/
  PASA: http://pasa.sourceforge.net/
  Cufflinks: http://cufflinks.cbcb.umd.edu/
  exonerate: http://www.ebi.ac.uk/~guy/exonerate/
  NCBI BLAST:  blast.ncbi.nlm.nih.gov/

Developed at the Genome Informatics Lab of Indiana University Biology Department