Identifying N\(^6\)-methyladenosine sites using extreme gradient boosting system optimized by particle swarm optimizer

DOI10.1016/J.JTBI.2019.01.035zbMath1409.92184OpenAlexW2913005526WikidataQ91316989 ScholiaQ91316989MaRDI QIDQ1730106

Minghao Yin, Xiaowei Zhao, Hongrui Zhang, Jinchao Ji, Ye Zhang, Qiao Ning

Publication date: 11 March 2019

Published in: Journal of Theoretical Biology (Search for Journal in Brave)

Full work available at URL: https://doi.org/10.1016/j.jtbi.2019.01.035

zbMATH Keywords

particle swarm optimizationextreme gradient boostingm\(^6\)A sitesN\(^6\)-methyladenosineXGboost

Mathematics Subject Classification ID

Approximation methods and heuristics in mathematical programming (90C59) Protein sequences, DNA sequences (92D20)

Uses Software

• Cell-PLoc
• pSuc-Lys
• XGBoost
• Prnam-PC
• iSuc-PseOpt
• iRSpot-PseDNC
• iRNA-Methyl
• iMethyl-PseAAC
• iSNO-AAPair
• iPTM-mLys
• pSumo-CD
• iCar-PseCp
• iHyd-PseCp
• iPhos-PseEvo
• iPhos-PseEn
• iRNA-AI
• pLoc-mAnimal
• pLoc-mVirus
• pLoc-mEuk
• iRNA-PseColl
• iRNA-2methyl
• iRNAm5C-PseDNC
• iRSpot-EL
• iPromoter-2L
• pLoc-mGneg
• pLoc-mPlant
• iKcr-PseEns
• iRNA-PseU
• iRNA-3typeA
• pLoc-mHum
• iDNA6mA-PseKNC
• iPPI-PseAAC
• 2L-piRNA
• iRO-3wPseKNC
• iHyd-PseAAC
• iRSpot-Pse6NC
• PSNO
• iLoc-lncRNA
• Fu-SulfPred

Cites Work

• pSuc-Lys: predict lysine succinylation sites in proteins with PseAAC and ensemble random forest approach
• Identifying 5-methylcytosine sites in RNA sequence using composite encoding feature into Chou's PseKNC
• Some remarks on protein attribute prediction and pseudo amino acid composition
• iMethyl-STTNC: identification of N\(^6\)-methyladenosine sites by extending the idea of SAAC into Chou's PseAAC to formulate RNA sequences
• iPPI-PseAAC(CGR): identify protein-protein interactions by incorporating chaos game representation into PseAAC
• Fu-SulfPred: identification of protein S-sulfenylation sites by fusing forests via Chou's general PseAAC
• Support-vector networks
• Nearest neighbor pattern classification

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