title: A method of precise mRNA/DNA homology-based gene structure prediction.
abstract: BACKGROUND
  Accurate and automatic gene finding and structural prediction is a common problem in bioinformatics, and applications need to be capable of handling non-canonical splice sites, micro-exons and partial gene structure predictions that span across several genomic clones.
  
  
  RESULTS
  We present a mRNA/DNA homology based gene structure prediction tool, GIGOgene. We use a new affine gap penalty splice-enhanced global alignment algorithm running in linear memory for a high quality annotation of splice sites. Our tool includes a novel algorithm to assemble partial gene structure predictions using interval graphs. GIGOgene exhibited a sensitivity of 99.08% and a specificity of 99.98% on the Genie learning set, and demonstrated a higher quality of gene structural prediction when compared to Sim4, est2genome, Spidey, Galahad and BLAT, including when genes contained micro-exons and non-canonical splice sites. GIGOgene showed an acceptable loss of prediction quality when confronted with a noisy Genie learning set simulating ESTs.
  
  
  CONCLUSIONS
  GIGOgene shows a higher quality of gene structure prediction for mRNA/DNA spliced alignment when compared to other available tools.
authors.affiliation: Department of Computer Science, College of Information Science and Technology, University of Nebraska, Omaha, NE 68182-0116, USA. achurbanov@mail.unomaha.edu
authors.forename: Alexander
authors.initials: A
authors.lastname: Churbanov
authors.forename: Mark
authors.initials: M
authors.lastname: Pauley
authors.forename: Daniel
authors.initials: D
authors.lastname: Quest
authors.forename: Hesham
authors.initials: H
authors.lastname: Ali
mesh_terms: D000465:Algorithms; D002999:Clone Cells / Q000737:chemistry; D004247:DNA / Q000737:chemistry*; D011237:Predictive Value of Tests; D012333:RNA, Messenger / Q000737:chemistry*; D016415:Sequence Alignment; D012689:Sequence Homology, Nucleic Acid; D012984:Software
chemical_list: D012333:RNA, Messenger; D004247:DNA