title: Improving gene recognition accuracy by combining predictions from two gene-finding programs.
abstract: BACKGROUND
  Despite constant improvements in prediction accuracy, gene-finding programs are still unable to provide automatic gene discovery with desired correctness. The current programs can identify up to 75% of exons correctly and less than 50% of predicted gene structures correspond to actual genes. New approaches to computational gene-finding are clearly needed.
  
  
  RESULTS
  In this paper we have explored the benefits of combining predictions from already existing gene prediction programs. We have introduced three novel methods for combining predictions from programs Genscan and HMMgene. The methods primarily aim to improve exon level accuracy of gene-finding by identifying more probable exon boundaries and by eliminating false positive exon predictions. This approach results in improved accuracy at both the nucleotide and exon level, especially the latter, where the average improvement on the newly assembled dataset is 7.9% compared to the best result obtained by Genscan and HMMgene. When tested on a long genomic multi-gene sequence, our method that maintains reading frame consistency improved nucleotide level specificity by 21.0% and exon level specificity by 32.5% compared to the best result obtained by either of the two programs individually.
  
  
  BACKGROUND
  The scripts implementing our methods are available from http://www.cs.ubc.ca/labs/beta/genefinding/
authors.affiliation: Computer Science Department, The University of California at Santa Cruz, Baskin Engineering, 95064, USA. rogic@cse.ucsc.edu
authors.forename: Sanja
authors.initials: S
authors.lastname: Rogic
authors.forename: B F Francis
authors.initials: BF
authors.lastname: Ouellette
authors.forename: Alan K
authors.initials: AK
authors.lastname: Mackworth
mesh_terms: D000465:Algorithms; D000818:Animals; D003205:Computing Methodologies; D004247:DNA / Q000235:genetics; D003628:Database Management Systems; D030541:Databases, Genetic; D018428:Drosophilidae / Q000235:genetics; D005091:Exons / Q000235:genetics*; D005189:False Positive Reactions; D006801:Humans; D016247:Information Storage and Retrieval / Q000379:methods*; D051379:Mice; D051381:Rats; D016364:Reading Frames / Q000235:genetics; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity; D016415:Sequence Alignment / Q000379:methods; D017421:Sequence Analysis / Q000379:methods*
chemical_list: D004247:DNA