生物学杂志

生物学杂志

• 技术方法 • 上一篇    下一篇

基于图形表示的减数分裂重组位点识别

  

  1. 渤海大学 数理学院, 锦州 121013
  • 出版日期:2017-12-18 发布日期:2017-12-18
  • 通讯作者: 李春,博士,教授,主要研究方向为食品安全与生物信息学，E-mail：lichwun@163.com
  • 作者简介:张一,硕士,主要研究方向为计算分子生物学,E-mail：798332334@qq.com
  • 基金资助:
    辽宁省自然科学基金项目（201602005）；辽宁省高等学校创新团队（LT2014024）；辽宁省食品安全重点实验室开放课题（LNSAKF2011034）

Identification of meiotic recombination spots based on the graphical representation

  1. College of Mathematics and Physics, Bohai University, Jinzhou 121013, China
  • Online:2017-12-18 Published:2017-12-18

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摘要： 减数分裂重组并非以统一的频率发生在基因组上, 而是在某些区域重组频率较高, 在另一些区域重组频率较低。减数分裂重组位点的刻画与识别对于认识重组机制具有重要意义。提出了一种新的DNA序列的3-D图形表示,并将其与Z-曲线相结合,借助正规化的ALE指标,用13维特征向量来刻画DNA序列进而进行减数分裂重组位点识别。以支持向量机作为分类器,利用夹克刀方法进行交互验证,所提方法的总精确度Acc达到了 93.70%,相关系数MCC达到了 0.873。这个结果表明此方法可作为减数分裂重组位点识别领域的一个有力工具。

关键词: 3-D图形表示, ALE指标, 减数分裂重组, 支持向量机

Abstract:

The meiotic recombination events do not occur with a uniform frequency throughout the genome but with a higher rate in some regions and lower in others. Characterization and identification of meiotic recombination spots is critical for our understanding of the recombination mechanism. In this paper, we first propose a new 3-D graphical representation for a DNA sequences. Then, combining the 3-D graphical representaion with Z-curve, we characterize a DNA sequence by a 13-D vector whose components are the corresponding normalized ALE indices. Support vector machine (SVM) and Jackknife cross-validation test are employed to perform our method on a benchmark dataset for recombination spots. Results show that our method achieved an overall accuracy of 93.70% with the Matthew′s correlation coefficient (MCC) of 0.873, which suggests that the proposed method can serve as a useful tool for identifying the recombination spots.

Key words: 3-D graphical representation, ALE-index, meiotic recombination, support vector machine