Journal of Food, Agriculture and Environment
Vol 8,
Issue 3&4,2010
Online ISSN: 1459-0263
Print ISSN: 1459-0255
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A hybrid Fisher/SVM method for SNP discovery in Brassica oilseed rape
Author(s):
Huijuan Xiong 1,
Xuehai Hu 1, Jingbo Xia 1, Ruiyuan Li 2, Feng Shi 1, Jinlin Meng 2, Zhi Li 1*Recieved Date: 2010-06-24, Accepted Date: 2010-10-27
Abstract:As genetic markers, single nucleotide polymorphisms play a crucial role in distinguishing most trait differences among individuals in a given species. The research on searching single nucleotide polymorphisms in kinds of organisms has been a hot topic in bio-informatics during the past ten years. In this paper, a hybrid Fisher/SVM SNPs identification algorithm is given for searching single nucleotide polymorphisms from sequences generated by Solexa GA in Brassica oilseed rape, which utilizes the advantage of traditional statistical test, specifically, Fisher exact test, and in conjunction with the notable prediction performance of support vector machine classifiers. By taking different windows width extracted from DNA sequences, the algorithm is designed to detect the single nucleotide polymorphisms in Brassica oilseed rape from a preview EU-China project. The results reveal that the new method is effective for single nucleotide polymorphisms detection in Brassica oilseed rape.
Keywords:Single nucleotide polymorphism prediction,
Brassica napus, Fisher exact test, Support vector machinesJournal: Journal of Food, Agriculture and Environment
Year: 2010
Volume: 8
Issue: 3&4
Category: Agriculture
Pages: 705-708
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