Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments
Brian J. Haas(Broad Institute), Steven L. Salzberg(University of Maryland, College Park), Wei Zhu(J. Craig Venter Institute), Mihaela Pertea(University of Maryland, College Park), Jonathan Allen(Lawrence Livermore National Laboratory), Joshua Orvis(Human Genome Sciences (United States)), Owen White(Human Genome Sciences (United States)), C. Robin Buell(J. Craig Venter Institute), Jennifer R. Wortman(Human Genome Sciences (United States))
Cited by 4,409Open Access
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.
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