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EvidentialGene : Evidence Directed Gene Construction for Eukaryotes

2014 Nov.: EvidentialGene sets are Best of clade in gene set completeness for 11 species of Arthropods, Plants and Fishes .
2014 June: Evigene gene-ome sets for Honey Bee and Deer Tick are publicly available.
2014 Feb. : Evigene sets for Cacao and Killifish are Best of clade for gene set completeness (size, orthology) for plants and fishes.

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[DIR] Parent Directory 04-Sep-2012 15:52 [DIR] about/ 25-Nov-2014 14:56 [DIR] arthropods/ 12-Nov-2014 13:12 [DIR] cacao/ 30-Jul-2014 13:32 [DIR] daphnia/ 12-Nov-2014 13:09 [DIR] evigene/ 24-Oct-2014 16:12 [DIR] killifish/ 30-Jul-2014 13:32 [DIR] nasonia/ 30-Jul-2014 13:32 [DIR] other/ 30-Jul-2014 13:32 [DIR] pea_aphid2/ 30-Jul-2014 13:32 [DIR] plants/ 06-Feb-2014 15:38 [DIR] vertebrates/ 10-Jun-2013 15:31

Folder evigene/ has this software, about/ describes this work, in posters and such documents. Most of the other folders contain gene-ome sets of animals and plants, constructed with EvidentialGene software. Some of these are genome-free, others are mixed genome-guided and mRNA-assembled.
 
2014: Honey Bee, Deer Tick and Water Flea gene-omes
with Evigene-mRNA

EvidentialGene mRNA Transcript Assembly Software

2013: Gene-omes built from mRNA-seq not genome DNA
Evigene-mRNA

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

2012: Perfect Genes Constructed with Gigabases of RNA

EvidentialGene Animal & Plant Genes Quality Comparison
evigenequal1


EvidentialGene :
Evidence Directed Gene Construction for Eukaryotes

  Don Gilbert, gilbertd at indiana edu, 2010 .. 2013
  http://arthropods.eugenes.org/EvidentialGene/

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 
assembly.

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 
evidence.

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