A hybrid Fisher/SVM method for SNP discovery in Brassica oilseed rape

作者：Xiong, Huijuan; Hu, Xuehai; Xia, Jingbo; Li, Ruiyuan; Shi, Feng; Meng, Jinlin; Li, Zhi^*

来源：Journal of Food Agriculture and Environment, 2010, 8(3-4): 705-708.

• Single nucleotide polymorphism prediction
• Brassica napus
• Fisher exact test
• Support vector machines

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.

• 出版日期2010-10
• 单位华中农业大学