Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments
Brian J. HaasJ Craig Venter Institute, The Institute for Genomic Research, Rockville, USASteven L. SalzbergCenter for Bioinformatics and Computational Biology, Department of Computer Science, 3125 Biomolecular Sciences Bldg #296, University of Maryland, College Park, Maryland 20742, USAWei ZhuJ Craig Venter Institute, The Institute for Genomic Research, Rockville, 9712 Medical Center Drive, Maryland 20850, USAMihaela PerteaCenter for Bioinformatics and Computational Biology, Department of Computer Science, 3125 Biomolecular Sciences Bldg #296, University of Maryland, College Park, Maryland 20742, USAJonathan AllenComputation Directorate, Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, California 94550, USAJoshua OrvisInstitute for Genome Sciences, University of Maryland Medical School, Baltimore, Maryland 21201, USAOwen WhiteJ Craig Venter Institute, The Institute for Genomic Research, Rockville, USAC. Robin BuellDepartment of Plant Biology, Michigan State University, East Lansing, USAJennifer R. WortmanJ Craig Venter Institute, The Institute for Genomic Research, Rockville, USA
2008en
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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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