华南农业大学学报2016，Vol.37Issue(3)：115-120,6.DOI:10.7671/j.issn.1001-411X.2016.03.018
一种二倍体片段测序中 SNP 检测系统的构建
Development of an automatic system for SNP detection in diploid fragment sequencing
摘要
Abstract
Objective] This study aims to develop a pattern-recognition based system for automatic single nucleotide polymorphism ( SNP ) detection in diploid fragment sequencing and improve the detection accuracy.[Method]The LabWindows/CVI 9.0 platform and Matlab environment were combined for ana-lyzing .ab1 or .scf files generated in diploid PCR fragment sequencing .Firstly, four bases G, A, T and C were separated for eliminating noise through one-dimensional discrete wavelet filtering , following with extraction of typical features of each base position ( peak ) from a fluorescence curve .A classifier based on back-propagation neural network was then used for SNP recognition and diagnosis .[Result] This es-tablished system was characterized by friendly interface , stable operation and manual modification acces-sibility .It classified the SNP reliability into six grades .Performance test with 143 SNPs of 26 sequencing fragments from Eucalyptus urophylla demonstrated that our system outperformed three previously reported software packages in detecting accuracy , false positive and false negative rates .[Conclusion] Our system has a high rate of accuracy without the need for a reference sequence .It could be used for efficient SNP detection in diploid PCR fragment sequencing .关键词
二倍体/测序/SNP检测/模式识别/尾叶桉Key words
diploid/sequencing/SNP detection/pattern recognition/Eucalyptus urophylla分类
信息技术与安全科学引用本文复制引用
邓继忠,林伟森,甘四明,黄华盛,李梅,金济,何明昊..一种二倍体片段测序中 SNP 检测系统的构建[J].华南农业大学学报,2016,37(3):115-120,6.基金项目
863计划（2013AA102705）；国家自然科学基金 （）
