Method
Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments
1 J Craig Venter Institute, The Institute for Genomic Research, Rockville, 9712 Medical Center Drive, Maryland 20850, USA
2 Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA
3 Center for Bioinformatics and Computational Biology, Department of Computer Science, 3125 Biomolecular Sciences Bldg #296, University of Maryland, College Park, Maryland 20742, USA
4 Computation Directorate, Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, California 94550, USA
5 Institute for Genome Sciences, University of Maryland Medical School, Baltimore, Maryland 21201, USA
6 Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824, USA
Genome Biology 2008, 9:R7 doi:10.1186/gb-2008-9-1-r7
Published: 11 January 2008Abstract
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.
