TY - GEN
T1 - Detection of m6A RNA Methylation in Nanopore Sequencing Data Using Support Vector Machine
AU - Jia, Shen
AU - Luo, Haochen
AU - Gao, Qiheng
AU - Guo, Jiaqi
AU - Su, Jionglong
AU - Meng, Jia
AU - Wu, Xiangyu
N1 - Publisher Copyright:
© 2019 IEEE.
PY - 2019/10
Y1 - 2019/10
N2 - N6-methyladenosine (m6A) is a prevalent internal modification in RNA which plays an important role in epitranscriptomics. The detection of m6A may be carried out by utilizing the Oxford Nanopore Technology (ONT) and machine learning. In this research, following a previous study by Liu et al, we hypothesize that the current intensitychange of the modification of the RNA(N6-methyladenosine) is the result of base-calling errors(mismatch frequency, deletion frequency, per-base quality and current intensity). We apply the Curlake, EpiNano software to divide the raw data into 5-mer sequences and extract features from the RNA sequence. The SVM classifier is used to verify this assumption. Our results confirmed the finding of a previous study by Liu et al, suggesting that the base-calling 'errors'may be usedto identify the N6-methyladenesine(m6A), and the consideration of the neighbourhood nucleotides of the 5mer will improve the accuracy of our prediction.
AB - N6-methyladenosine (m6A) is a prevalent internal modification in RNA which plays an important role in epitranscriptomics. The detection of m6A may be carried out by utilizing the Oxford Nanopore Technology (ONT) and machine learning. In this research, following a previous study by Liu et al, we hypothesize that the current intensitychange of the modification of the RNA(N6-methyladenosine) is the result of base-calling errors(mismatch frequency, deletion frequency, per-base quality and current intensity). We apply the Curlake, EpiNano software to divide the raw data into 5-mer sequences and extract features from the RNA sequence. The SVM classifier is used to verify this assumption. Our results confirmed the finding of a previous study by Liu et al, suggesting that the base-calling 'errors'may be usedto identify the N6-methyladenesine(m6A), and the consideration of the neighbourhood nucleotides of the 5mer will improve the accuracy of our prediction.
KW - N6-methyladenosine
KW - Oxford Nanopore Technology
KW - support vector machine
UR - http://www.scopus.com/inward/record.url?scp=85079132747&partnerID=8YFLogxK
U2 - 10.1109/CISP-BMEI48845.2019.8965760
DO - 10.1109/CISP-BMEI48845.2019.8965760
M3 - Conference Proceeding
AN - SCOPUS:85079132747
T3 - Proceedings - 2019 12th International Congress on Image and Signal Processing, BioMedical Engineering and Informatics, CISP-BMEI 2019
BT - Proceedings - 2019 12th International Congress on Image and Signal Processing, BioMedical Engineering and Informatics, CISP-BMEI 2019
A2 - Li, Qingli
A2 - Wang, Lipo
PB - Institute of Electrical and Electronics Engineers Inc.
T2 - 12th International Congress on Image and Signal Processing, BioMedical Engineering and Informatics, CISP-BMEI 2019
Y2 - 19 October 2019 through 21 October 2019
ER -