GenePRIMP: A GENE PRediction IMprovement Pipeline for Prokaryotic genomes

Journal Article · Thu Apr 01 00:00:00 EDT 2010 · Nature Methods

DOI:https://doi.org/10.1038/nmeth.1457· OSTI ID:1032520

Pati, Amrita; Ivanova, Natalia N; Mikhailova, Natalia; Ovchinnikova, Galina; Hooper, Sean D; Lykidis, Athanasios; Kyrpides, Nikos C

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.

• Research Organization: Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
• Sponsoring Organization: Genomics Division
• DOE Contract Number: DE-AC02-05CH11231
• OSTI ID: 1032520
• Report Number(s): LBNL-3419E; TRN: US201202%%246
• Journal Information: Nature Methods, Vol. 7, Issue 6; ISSN 1548-7091
• Country of Publication: United States
• Language: English

Related Subjects

59 BASIC BIOLOGICAL SCIENCES
99 GENERAL AND MISCELLANEOUS//MATHEMATICS, COMPUTING, AND INFORMATION SCIENCE
EVALUATION
FORECASTING
GENES