Work

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

Year: 2008

Type: article

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.

Source: Genome biology

DOI: 10.1186/gb-2008-9-1-r7

Authors: Brian J Haas, Steven L Salzberg, Wei Zhu, Mihaela Pertea, Jonathan E Allen, Joshua Orvis, Owen White, C Robin Buell, Jennifer R Wortman

Institutions: Broad Institute, J. Craig Venter Institute, University of Maryland, College Park, Lawrence Livermore National Laboratory, University of Maryland, Baltimore, Michigan State University

Language: English

Topic: Genomics and Phylogenetic Studies

Subfield: Molecular Biology

Field: Biochemistry, Genetics and Molecular Biology

Domain: Life Sciences

Open Access status: gold

Estimated APC paid: $5,490

Funders: National Science Foundation, National Institutes of Health, National Institute of General Medical Sciences, U.S. National Library of Medicine

Awards: Computational Gene Modeling and Genome Sequence Assembly, An Annotation Resource for the Rice Genome, Bioinformatics Software for Analyzing Microbial Genomes

OpenAlex ID: W2108108770

FWCI: 5.192

Cites: 49

Cited by: 4,046

Related to: 10