GenePRIMP: a gene prediction improvement pipeline for prokaryotic genomes.
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.
Pati
Amrita
A
Genome Biology Program, Department of Energy, Joint Genome Institute, Walnut Creek, California, USA. apati@lbl.gov
Ivanova
Natalia N
NN
Mikhailova
Natalia
N
Ovchinnikova
Galina
G
Hooper
Sean D
SD
Lykidis
Athanasios
A
Kyrpides
Nikos C
NC
D019295:Computational Biology / Q000379:methods*; D020745:Genome, Archaeal; D016680:Genome, Bacterial; D008957:Models, Genetic