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

Genome Biol. 2008 Jan 11;9(1):R7. doi: 10.1186/gb-2008-9-1-r7.


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.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Computational Biology / methods*
  • Databases, Genetic
  • Eukaryota / genetics
  • Gene Components*
  • Genome, Human / genetics*
  • Genome, Plant / genetics*
  • Humans
  • Oryza
  • Protein Isoforms / genetics*
  • Software


  • Protein Isoforms