InDel marker detection by integration of multiple softwares using machine learning techniques.
BACKGROUND
In the biological experiments of soybean species, molecular markers are widely used to verify the soybean genome or construct its genetic map. Among a variety of molecular markers, insertions and deletions (InDels) are preferred with the advantages of wide distribution and high density at the whole-genome level. Hence, the problem of detecting InDels based on next-generation sequencing data is of great importance for the design of InDel markers. To tackle it, this paper integrated machine learning techniques with existing software and developed two algorithms for InDel detection, one is the best F-score method (BF-M) and the other is the Support Vector Machine (SVM) method (SVM-M), which is based on the classical SVM model.


RESULTS
The experimental results show that the performance of BF-M was promising as indicated by the high precision and recall scores, whereas SVM-M yielded the best performance in terms of recall and F-score. Moreover, based on the InDel markers detected by SVM-M from soybeans that were collected from 56 different regions, highly polymorphic loci were selected to construct an InDel marker database for soybean.


CONCLUSIONS
Compared to existing software tools, the two algorithms proposed in this work produced substantially higher precision and recall scores, and remained stable in various types of genomic regions. Moreover, based on SVM-M, we have constructed a database for soybean InDel markers and published it for academic research.
School of Computer Science and Technology, Wuhan University of Technology, Wuhan, China.
Jianqiu
J
Yang
School of Computer Science and Technology, Heilongjiang University, Harbin, China.
Xinyi
X
Shi
School of Computer Science and Technology, Wuhan University of Technology, Wuhan, China.
Lun
L
Hu
School of Computer Science and Technology, Wuhan University of Technology, Wuhan, China.
Daipeng
D
Luo
School of Computer Science and Technology, Wuhan University of Technology, Wuhan, China.
Jing
J
Peng
School of Computer Science and Technology, Wuhan University of Technology, Wuhan, China.
Shengwu
S
Xiong
The Key Lab of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China.
Fanjing
F
Kong
The Key Lab of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China.
Baohui
B
Liu
The Key Lab of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China. yuanxh@iga.ac.cn.
Xiaohui
X
Yuan
Evaluation; InDel detection; Insertions and deletions