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Please use this identifier to cite or link to this item: http://hdl.handle.net/10397/5113

Title: UPDG: Utilities package for data analysis of Pooled DNA GWAS
Authors: Ho, Daniel W. H.
Yap, Keng-hung Maurice
Yip, Shea-ping
Subjects: Computer software
DNA
Genomes
Computer and software stores
Issue Date: 17-Jan-2012
Publisher: BioMed Central Ltd.
Citation: BMC genetics, 2012, v. 13, 1, p. 1-6.
Abstract: Background: Despite being a well-established strategy for cost reduction in disease gene mapping, pooled DNA association study is much less popular than the individual DNA approach. This situation is especially true for pooled DNA genomewide association study (GWAS), for which very few computer resources have been developed for its data analysis. This motivates the development of UPDG (Utilities package for data analysis of Pooled DNA GWAS).
Results: UPDG represents a generalized framework for data analysis of pooled DNA GWAS with the integration of Unix/Linux shell operations, Perl programs and R scripts. With the input of raw intensity data from GWAS, UPDG performs the following tasks in a stepwise manner: raw data manipulation, correction for allelic preferential amplification, normalization, nested analysis of variance for genetic association testing, and summarization of analysis results. Detailed instructions, procedures and commands are provided in the comprehensive user manual describing the whole process from preliminary preparation of software installation to final outcome acquisition. An example dataset (input files and sample output files) is also included in the package so that users can easily familiarize themselves with the data file formats, working procedures and expected output. Therefore, UPDG is especially useful for users with some computer knowledge, but without a sophisticated programming background.
Conclusions: UPDG provides a free, simple and platform-independent one-stop service to scientists working on pooled DNA GWAS data analysis, but with less advanced programming knowledge. It is our vision and mission to reduce the hindrance for performing data analysis of pooled DNA GWAS through our contribution of UPDG. More importantly, we hope to promote the popularity of pooled DNA GWAS, which is a very useful research strategy.
Description: DOI: 10.1186/1471-2156-13-1
Rights: © 2012 Ho et al; licensee 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.
Type: Journal/Magazine Article
URI: http://hdl.handle.net/10397/5113
ISSN: 1471-2156
Appears in Collections:SO Journal/Magazine Articles

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