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

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

Research output: Contribution to journalArticlepeer-review

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.

Original languageEnglish (US)
Article numberR7
JournalGenome biology
Volume9
Issue number1
DOIs
StatePublished - Jan 11 2008
Externally publishedYes

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Genetics
  • Cell Biology

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