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Title: 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:
 [1];  [2];  [2];  [2];  [2];  [2]
  1. LBNL/JGI
  2. 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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