Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments

Brian J Haas¹^,2 , Steven L Salzberg³ , Wei Zhu¹ , Mihaela Pertea³ , Jonathan E Allen³^,4 , Joshua Orvis¹^,5 , Owen White¹^,5 , C Robin Buell¹^,6 and Jennifer R Wortman¹^,5

¹J Craig Venter Institute, The Institute for Genomic Research, Rockville, 9712 Medical Center Drive, Maryland 20850, USA

²Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA

³Center for Bioinformatics and Computational Biology, Department of Computer Science, 3125 Biomolecular Sciences Bldg #296, University of Maryland, College Park, Maryland 20742, USA

⁴Computation Directorate, Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, California 94550, USA

⁵Institute for Genome Sciences, University of Maryland Medical School, Baltimore, Maryland 21201, USA

⁶Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824, USA

author email corresponding author email

Genome Biology 2008, 9:R7doi:10.1186/gb-2008-9-1-r7


Published:	11 January 2008

Subject areas: Bioinformatics, Genome studies, Methods

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.