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