EvidentialGene :
Evidence Directed Gene predictions
for Eukaryotes

  Don Gilbert, gilbertd at indiana edu  
  Summer-fall 2010
  See http://arthropods.eugenes.org/genes2/

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/