A Support Vector Machine Based Method to Predict Success for Polymerase Chain Reactions

Author(s): Xiaoqing Yu, Xiaoqi Zheng, Liangyu Meng, Chun Li, Jun Wang.

Journal Name: Combinatorial Chemistry & High Throughput Screening

Volume 15 , Issue 6 , 2012

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Abstract:

Polymerase chain reaction (PCR) is one of the most popular molecular biological techniques and has been widely applied in many areas. However, PCR still faces challenges nowadays. During recent decades, the experimental procedure of PCR, including the primer design, was always the focus of attention, while little attention was paid to the analysis of the PCR template, and still nobody can accurately predict whether or not a DNA sequence can be simply amplified using conventional Taq DNA polymerase-based PCR protocol. In this study, we focus on the DNA template, the subject of PCR experiment, and introduce a support vector machine (SVM) based method to help evaluate PCR result. Through the Jackknife cross-validation test, our method achieves an accuracy of 92.06%, with 93.62% sensitivity and 90.53% specificity.

Keywords: Amplicon, DNA template, k-mers, PCR success, polymerase chain reactions, support vector machines, primer design, DNA sequence, gene manipulation, amplicon, receiver operating characteristic

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Article Details

VOLUME: 15
ISSUE: 6
Year: 2012
Page: [486 - 491]
Pages: 6
DOI: 10.2174/138620712800563936
Price: $58

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