GenePRIMP: a gene prediction improvement pipeline for prokaryotic genomes

Nat Methods. 2010 Jun;7(6):455-7. doi: 10.1038/nmeth.1457. Epub 2010 May 2.


We present 'gene prediction improvement pipeline' (GenePRIMP;, a computational process that performs evidence-based evaluation of gene models in prokaryotic genomes and reports anomalies including inconsistent start sites, missed genes and split genes. We found that manual curation of gene models using the anomaly reports generated by GenePRIMP improved their quality, and demonstrate the applicability of GenePRIMP in improving finishing quality and comparing different genome-sequencing and annotation technologies.

Publication types

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

MeSH terms

  • Computational Biology / methods*
  • Genome, Archaeal*
  • Genome, Bacterial*
  • Models, Genetic