GenePRIMP: A Gene Prediction Improvement Pipeline For Prokaryotic Genomes

Software · Thu Jul 08 04:00:00 EDT 2010

OSTI ID:1431050

Kyrpides, Nikos C. ^[1]; Ivanova, Natalia N. ^[2]; Pati, Amrita ^[2]; Ovchinnikova, Galina ^[2]; Lykidis, Athanasios ^[2]; Mikhailova, Natalia ^[2]

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1. LBNL/JGI
2. LBNL

GenePRIMP (Gene Prediction Improvement Pipeline, 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, missing genes, and split genes. We show that manual curation of gene models using the anomaly reports generated by GenePRIMP improves their quality and demonstrate the applicability of GenePRIMP in improving finishing quality and comparing different genome sequencing and annotation technologies. Keywords in context: Gene model, Quality Control, Translation start sites, Automatic correction. Hardware requirements; PC, MAC; Operating System: UNIX/LINUX; Compiler/Version: Perl 5.8.5 or higher; Special requirements: NCBI Blast and nr installation; File Types: Source Code, Executable module(s), Sample problem input data; installation instructions other; programmer documentation. Location/transmission: http://geneprimp.jgi-psf.org/gp.tar.gz

• Short Name / Acronym: GenePRIMP; 005653WKSTN00
• Site Accession Number: 2857
• Version: 00
• Programming Language(s): Medium: X; OS: Unix/Linux
• Research Organization: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
• Sponsoring Organization: USDOE, LBNL-DOE Operations
• Contributing Organization: LBNL-DOE Operations
• DOE Contract Number: AC02-05CH11231
• OSTI ID: 1431050
• Country of Origin: United States