GenePRIMP: A Gene Prediction Improvement Pipeline For Prokaryotic Genomes
Abstract
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
- Authors:
-
- LBNL/JGI
- LBNL
- Publication Date:
- Research Org.:
- Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
- Sponsoring Org.:
- USDOE, LBNL-DOE Operations
- Contributing Org.:
- LBNL-DOE Operations
- OSTI Identifier:
- 1431050
- Report Number(s):
- GenePRIMP; 005653WKSTN00
R&D Project: KP1605020; 2857
- DOE Contract Number:
- AC02-05CH11231
- Resource Type:
- Software
- Software Revision:
- 00
- Software Package Number:
- 005653
- Software CPU:
- WKSTN
- Source Code Available:
- Yes
- Other Software Info:
- LBNL RESERVES ALL RIGHTS TO DISTRIBUTE THE SOFTWARE
- Country of Publication:
- United States
Citation Formats
Kyrpides, Nikos C., Ivanova, Natalia N., Pati, Amrita, Ovchinnikova, Galina, Lykidis, Athanasios, and Mikhailova, Natalia. GenePRIMP: A Gene Prediction Improvement Pipeline For Prokaryotic Genomes.
Computer software. Vers. 00. USDOE, LBNL-DOE Operations. 8 Jul. 2010.
Web.
Kyrpides, Nikos C., Ivanova, Natalia N., Pati, Amrita, Ovchinnikova, Galina, Lykidis, Athanasios, & Mikhailova, Natalia. (2010, July 8). GenePRIMP: A Gene Prediction Improvement Pipeline For Prokaryotic Genomes (Version 00) [Computer software].
Kyrpides, Nikos C., Ivanova, Natalia N., Pati, Amrita, Ovchinnikova, Galina, Lykidis, Athanasios, and Mikhailova, Natalia. GenePRIMP: A Gene Prediction Improvement Pipeline For Prokaryotic Genomes.
Computer software. Version 00. July 8, 2010.
@misc{osti_1431050,
title = {GenePRIMP: A Gene Prediction Improvement Pipeline For Prokaryotic Genomes, Version 00},
author = {Kyrpides, Nikos C. and Ivanova, Natalia N. and Pati, Amrita and Ovchinnikova, Galina and Lykidis, Athanasios and Mikhailova, Natalia},
abstractNote = {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},
doi = {},
url = {https://www.osti.gov/biblio/1431050},
year = {Thu Jul 08 00:00:00 EDT 2010},
month = {Thu Jul 08 00:00:00 EDT 2010},
note =
}
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