title: Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments.
abstract: EVidenceModeler (EVM) is presented as an automated eukaryotic gene structure annotation tool that reports eukaryotic gene structures as a weighted consensus of all available evidence. EVM, when combined with the Program to Assemble Spliced Alignments (PASA), yields a comprehensive, configurable annotation system that predicts protein-coding genes and alternatively spliced isoforms. Our experiments on both rice and human genome sequences demonstrate that EVM produces automated gene structure annotation approaching the quality of manual curation.
authors.affiliation: J Craig Venter Institute, The Institute for Genomic Research, Rockville, Maryland 20850, USA. bhaas@broad.mit.edu
authors.forename: Brian J
authors.initials: BJ
authors.lastname: Haas
authors.forename: Steven L
authors.initials: SL
authors.lastname: Salzberg
authors.forename: Wei
authors.initials: W
authors.lastname: Zhu
authors.forename: Mihaela
authors.initials: M
authors.lastname: Pertea
authors.forename: Jonathan E
authors.initials: JE
authors.lastname: Allen
authors.forename: Joshua
authors.initials: J
authors.lastname: Orvis
authors.forename: Owen
authors.initials: O
authors.lastname: White
authors.forename: C Robin
authors.initials: CR
authors.lastname: Buell
authors.forename: Jennifer R
authors.initials: JR
authors.lastname: Wortman
mesh_terms: D019295:Computational Biology / Q000379:methods*; D030541:Databases, Genetic; D056890:Eukaryota / Q000235:genetics; D040461:Gene Components; D015894:Genome, Human / Q000235:genetics*; D018745:Genome, Plant / Q000235:genetics*; D006801:Humans; D012275:Oryza; D020033:Protein Isoforms / Q000235:genetics*; D012984:Software
chemical_list: D020033:Protein Isoforms