PDA: Pooled DNA analyzer.

BMC Bioinformatics
Hsin-Chou YangCathy S J Fann

Abstract

Association mapping using abundant single nucleotide polymorphisms is a powerful tool for identifying disease susceptibility genes for complex traits and exploring possible genetic diversity. Genotyping large numbers of SNPs individually is performed routinely but is cost prohibitive for large-scale genetic studies. DNA pooling is a reliable and cost-saving alternative genotyping method. However, no software has been developed for complete pooled-DNA analyses, including data standardization, allele frequency estimation, and single/multipoint DNA pooling association tests. This motivated the development of the software, 'PDA' (Pooled DNA Analyzer), to analyze pooled DNA data. We develop the software, PDA, for the analysis of pooled-DNA data. PDA is originally implemented with the MATLAB language, but it can also be executed on a Windows system without installing the MATLAB. PDA provides estimates of the coefficient of preferential amplification and allele frequency. PDA considers an extended single-point association test, which can compare allele frequencies between two DNA pools constructed under different experimental conditions. Moreover, PDA also provides novel chromosome-wide multipoint association tests based on p-value co...Continue Reading

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Citations

Jan 7, 2009·Genetics Research·Matti PirinenMikko J Sillanpää
Apr 17, 2008·BMC Bioinformatics·Hsin-Chou YangCathy S J Fann
Mar 21, 2007·BMC Genomics·Stefan WilkeningFederico Canzian
Oct 6, 2017·Briefings in Bioinformatics·Chia-Wei Chen, Hsin-Chou Yang

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Methods Mentioned

BETA
genotyping

Software Mentioned

PDA
MS Windows
MS
MATLAB71
SWEPT
Pooled DNA Analyzer ( PDA )
MATLAB
Windows
MathType

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