We present 'gene prediction improvement pipeline' (GenePRIMP; http://geneprimp.jgi-psf.org/), 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.
Subscribe to Journal
Get full journal access for 1 year
only $20.17 per issue
All prices are NET prices.
VAT will be added later in the checkout.
Rent or Buy article
Get time limited or full article access on ReadCube.
All prices are NET prices.
Benson, D.A., Karsch-Mizrachi, I., Lipman, D.J., Ostell, J. & Sayers, E.W. Nucleic Acids Res. 38, D46–D51 (2010).
Ishino, Y., Okada, H., Ikeuchi, M. & Taniguchi, H. Proteomics 7, 4053–4065 (2007).
Smollett, K.L. et al. Microbiology 155, 186–197 (2009).
Kyrpides, N.C. Nat. Biotechnol. 27, 627–632 (2009).
Hyatt, D. et al. BMC Bioinformatics (in the press).
Besemer, J., Lomsadze, A. & Borodovsky, M. Nucleic Acids Res. 29, 2607–2618 (2001).
Delcher, A.L., Bratke, K.A., Powers, E.C. & Salzberg, S.L. Bioinformatics 23, 673–679 (2007).
Zhu, H.Q., Hu, G.Q., Quyang, Z.Q., Wang, J. & She, Z.S. Bioinformatics 20, 3308–3317 (2004).
Tech, M. & Meinicke, P. BMC Bioinformatics 7, 121 (2006).
Yu, G.X. et al. Nucleic Acids Res. 35, 3953–3962 (2007).
Nagy, A. et al. BMC Bioinformatics 9, 353 (2008).
Castellana, N.E. et al. Proc. Natl. Acad. Sci. USA 105, 21034–21038 (2008).
Markowitz, V.M. et al. Nucleic Acids Res. 38, D382–D390 (2010).
Aziz, R.K. et al. BMC Genomics 9, 75 (2008).
Bocs, S., Cruveiller, S., Vallenet, D., Nuel, G. & Medigue, C. Nucleic Acids Res. 31, 3723–3726 (2003).
We acknowledge the help and support of I. Anderson, K. Mavromatis, X. Zhao and V. Markowitz. GenePRIMP was developed under the auspices of the US Department of Energy′s Office of Science, Biological and Environmental Research Program and by the University of California, Lawrence Berkeley National Laboratory under contract DE-AC02-05CH11231, Lawrence Livermore National Laboratory under contract DE-AC52-07NA27344 and Los Alamos National Laboratory under contract DE-AC02-06NA25396. Validation and improvement of the system was supported by US National Institutes of Health Data Analysis and Coordination Center contract U01-HG004866. The work conducted by the US Department of Energy Joint Genome Institute is supported by the Office of Science of the US. Department of Energy under contract DE-AC02-05CH11231.
The authors declare no competing financial interests.
About this article
Cite this article
Pati, A., Ivanova, N., Mikhailova, N. et al. GenePRIMP: a gene prediction improvement pipeline for prokaryotic genomes. Nat Methods 7, 455–457 (2010) doi:10.1038/nmeth.1457
Whole-genome sequence data and analysis of Lactobacillus delbrueckii subsp. lactis ACA-DC 178 isolated from Greek Kasseri cheese
Data in Brief (2019)
Genome Research (2019)
Biomass and Bioenergy (2019)
Genome expansion of an obligate parthenogenesis-associated Wolbachia poses an exception to the symbiont reduction model
BMC Genomics (2019)
International Journal of Systematic and Evolutionary Microbiology (2019)