i6mA-Fuse: improved and robust prediction of DNA 6 mA sites in the Rosaceae genome by fusing multiple feature representation

Plant Molecular Biology
Md Mehedi HasanHiroyuki Kurata

Abstract

DNA N6-methyladenine (6 mA) is one of the most vital epigenetic modifications and involved in controlling the various gene expression levels. With the avalanche of DNA sequences generated in numerous databases, the accurate identification of 6 mA plays an essential role for understanding molecular mechanisms. Because the experimental approaches are time-consuming and costly, it is desirable to develop a computation model for rapidly and accurately identifying 6 mA. To the best of our knowledge, we first proposed a computational model named i6mA-Fuse to predict 6 mA sites from the Rosaceae genomes, especially in Rosa chinensis and Fragaria vesca. We implemented the five encoding schemes, i.e., mononucleotide binary, dinucleotide binary, k-space spectral nucleotide, k-mer, and electron-ion interaction pseudo potential compositions, to build the five, single-encoding random forest (RF) models. The i6mA-Fuse uses a linear regression model to combine the predicted probability scores of the five, single encoding-based RF models. The resultant species-specific i6mA-Fuse achieved remarkably high performances with AUCs of 0.982 and 0.978 and with MCCs of 0.869 and 0.858 on the independent datasets of Rosa chinensis and Fragaria vesca, r...Continue Reading

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Citations

Sep 24, 2020·Journal of Computer-aided Molecular Design·Mst Shamima KhatunHiroyuki Kurata
Oct 20, 2020·Current Genomics·Md Mamunur RashidHiroyuki Kurata
Nov 25, 2020·Briefings in Bioinformatics·Balachandran ManavalanGwang Lee
Oct 24, 2020·Current Genomics·Mst Shamima KhatunHiroyuki Kurata
Apr 24, 2020·Computational and Structural Biotechnology Journal·Md Mehedi HasanHiroyuki Kurata
Jan 26, 2021·Briefings in Functional Genomics·Md Mehedi HasanBalachandran Manavalan
Nov 17, 2020·Frontiers in Cell and Developmental Biology·Yixiao ZhaiYuming Zhao
Nov 25, 2020·Molecular Therapy. Nucleic Acids·Balachandran ManavalanGwang Lee
Apr 4, 2021·International Journal of Molecular Sciences·Andi Nur NilamyaniHiroyuki Kurata
May 9, 2021·Briefings in Bioinformatics·Phasit CharoenkwanWatshara Shoombuatong

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Methods Mentioned

BETA
PCR

Software Mentioned

SVM light package
R
i6mA
Kmer
Fuse
WEKA
randomForest
CD
PERL
vesca

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