DraGnET: Software for storing, managing and analyzing annotated draft genome sequence data

BMC Bioinformatics

Software

Ruchita Sirkanungo¹  Leslie Miller²  Stacy Duncan³  Gregory J Phillips³ 

[1] Department of Computer Science, Iowa State University, Ames, Iowa, USA;Department of Computer Science, Iowa State University, Ames, Iowa, USA;Interdepartmental Bioinformatics and Computational Biology, Iowa State University, Ames, Iowa, USA;Department of Veterinary Microbiology and Preventive Medicine, Iowa State University, Ames, Iowa, USA;Interdepartmental Bioinformatics and Computational Biology, Iowa State University, Ames, Iowa, USA;

关键词: Basic Local Alignment Search Tool;    Genome Sequence Data;    Integrate Microbial Genome;    Reverse Vaccinology;    Strain Information;   

DOI  :  10.1186/1471-2105-11-100

 received in 2009-10-08, accepted in 2010-02-22,  发布年份 2010

来源: Springer

【 摘 要 】

BackgroundNew "next generation" DNA sequencing technologies offer individual researchers the ability to rapidly generate large amounts of genome sequence data at dramatically reduced costs. As a result, a need has arisen for new software tools for storage, management and analysis of genome sequence data. Although bioinformatic tools are available for the analysis and management of genome sequences, limitations still remain. For example, restrictions on the submission of data and use of these tools may be imposed, thereby making them unsuitable for sequencing projects that need to remain in-house or proprietary during their initial stages. Furthermore, the availability and use of next generation sequencing in industrial, governmental and academic environments requires biologist to have access to computational support for the curation and analysis of the data generated; however, this type of support is not always immediately available.ResultsTo address these limitations, we have developed DraGnET (Draft Genome Evaluation Tool). DraGnET is an open source web application which allows researchers, with no experience in programming and database management, to setup their own in-house projects for storing, retrieving, organizing and managing annotated draft and complete genome sequence data. The software provides a web interface for the use of BLAST, allowing users to perform preliminary comparative analysis among multiple genomes. We demonstrate the utility of DraGnET for performing comparative genomics on closely related bacterial strains. Furthermore, DraGnET can be further developed to incorporate additional tools for more sophisticated analyses.ConclusionsDraGnET is designed for use either by individual researchers or as a collaborative tool available through Internet (or Intranet) deployment. For genome projects that require genome sequencing data to initially remain proprietary, DraGnET provides the means for researchers to keep their data in-house for analysis using local programs or until it is made publicly available, at which point it may be uploaded to additional analysis software applications. The DraGnET home page is available at http://www.dragnet.cvm.iastate.edu and includes example files for examining the functionalities, a link for downloading the DraGnET setup package and a link to the DraGnET source code hosted with full documentation on SourceForge.

【 授权许可】

Unknown   
© Duncan et al; licensee BioMed Central Ltd. 2010. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.