Haas, Brian U.Salzberg, Steven L.Zhu, WeiPertea, MihaelaAllen, Jonathan E.Orvis, JoshuaWhite, OwenBuell, C RobinWortman, Jennifer REVidenceModeler (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.en-USEVidenceModeler (EVM)automated eukaryotic gene structure annotation toolProgram to Assemble Spliced Alignments (PASA)manual curationArticle