title: Evaluation of gene prediction software using a genomic data set: application to Arabidopsis thaliana sequences.
abstract: BACKGROUND
  The annotation of the Arabidopsis thaliana genome remains a problem in terms of time and quality. To improve the annotation process, we want to choose the most appropriate tools to use inside a computer-assisted annotation platform. We therefore need evaluation of prediction programs with Arabidopsis sequences containing multiple genes.
  
  
  RESULTS
  We have developed AraSet, a data set of contigs of validated genes, enabling the evaluation of multi-gene models for the Arabidopsis genome. Besides conventional metrics to evaluate gene prediction at the site and the exon levels, new measures were introduced for the prediction at the protein sequence level as well as for the evaluation of gene models. This evaluation method is of general interest and could apply to any new gene prediction software and to any eukaryotic genome. The GeneMark.hmm program appears to be the most accurate software at all three levels for the Arabidopsis genomic sequences. Gene modeling could be further improved by combination of prediction software.
  
  
  BACKGROUND
  The AraSet sequence set, the Perl programs and complementary results and notes are available at http://sphinx.rug.ac.be:8080/biocomp/napav/.
  
  
  BACKGROUND
  Pierre.Rouze@gengenp.rug.ac.be.
authors.affiliation: Laboratoire associé de l'INRA, France.
authors.forename: N
authors.initials: N
authors.lastname: Pavy
authors.forename: S
authors.initials: S
authors.lastname: Rombauts
authors.forename: P
authors.initials: P
authors.lastname: Déhais
authors.forename: C
authors.initials: C
authors.lastname: Mathé
authors.forename: D V
authors.initials: DV
authors.lastname: Ramana
authors.forename: P
authors.initials: P
authors.lastname: Leroy
authors.forename: P
authors.initials: P
authors.lastname: Rouzé
mesh_terms: D017398:Alternative Splicing / Q000235:genetics; D017360:Arabidopsis / Q000235:genetics*; D019295:Computational Biology / Q000379:methods*; D020451:Contig Mapping / Q000379:methods; D016208:Databases, Factual; D005069:Evaluation Studies as Topic; D005091:Exons / Q000235:genetics; D018745:Genome, Plant; D008957:Models, Genetic; D015203:Reproducibility of Results; D017422:Sequence Analysis, DNA / Q000379:methods*; D020539:Sequence Analysis, Protein; D012986:Software Validation