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PredictFP2: A New Computational Model to Predict Fusion Peptide Domain in All Retroviruses

文献类型：期刊论文

作者Wu, Sijia1; Wu, Xiaoming1; Tian, Jie3; Zhou, Xiaobo2; Huang, Liyu1
刊名IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS
出版日期2020-09-01
卷号17期号:5页码:1714-1720
关键词Benchmark testing Amino acids Support vector machines Computational modeling Predictive models Cells (biology) Databases Fusion peptide prediction FP distribution hydrophobicity retrovirus support vector machine
ISSN号1545-5963
DOI10.1109/TCBB.2019.2898943
通讯作者Wu, Sijia(wusjia@xidian.edu.cn) ; Huang, Liyu(huangly@mail.xidian.edu.cn)
英文摘要Fusion peptide (FP) is a pivotal domain for the entry of retrovirus into host cells to continue self-replication. The crucial role indicates that FP is a promising drug target for therapeutic intervention. A FP model proposed in our previous work is relatively not efficient to predict FP in retroviruses. Thus in this work, we come up with a new computational model to predict FP domains in all the retroviruses. It basically predicts FP domains through recognizing their start and end sites separately with SVM method combing the hydrophobicity knowledge of the subdomain around furin cleavage site. The classification accuracy rates are 91.91, 91.20 and 89.13 percent respectively corresponding to jack-knife, 10-fold cross-validation and 5-fold cross-validation test. Second, this model discovered 69,753 and 493 putative FPs after scanning amino acid sequences and HERV DNA sequences both without FP annotations. Subsequently, a statistical analysis was performed on the 69,753 putative FP sequences, which confirms that FP is a hydrophobic domain. Lastly, we depicted the distribution of the 493 putative FP sequences on each human chromosome and each HERV family, which shows that FP of HERV probably has chromosome and family preference.
资助项目National Key Research and Development Program of China[2017YFA0205202] ; China Postdoctoral Science Foundation[2018M643583] ; Fundamental Research Funds for the Central Universities - National Natural Science Foundation of China[61672422] ; Fundamental Research Funds for the Central Universities - National Natural Science Foundation of China[U1401255]
WOS研究方向Biochemistry & Molecular Biology ; Computer Science ; Mathematics
语种英语
WOS记录号WOS:000576418300023
出版者IEEE COMPUTER SOC
资助机构National Key Research and Development Program of China ; China Postdoctoral Science Foundation ; Fundamental Research Funds for the Central Universities - National Natural Science Foundation of China
源URL[http://ir.ia.ac.cn/handle/173211/42075]  
专题自动化研究所_中国科学院分子影像重点实验室
通讯作者Wu, Sijia; Huang, Liyu
作者单位1.Xidian Univ, Sch Life Sci & Technol, Xian 710049, Shaanxi, Peoples R China
2.Wake Forest Sch Med, Dept Radiol, Med Ctr Blvd, Winston Salem, NC 27157 USA
3.Chinese Acad Sci, Inst Automat, Beijing, Peoples R China
推荐引用方式
GB/T 7714		 Wu, Sijia,Wu, Xiaoming,Tian, Jie,et al. PredictFP2: A New Computational Model to Predict Fusion Peptide Domain in All Retroviruses[J]. IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS,2020,17(5):1714-1720.
APA Wu, Sijia,Wu, Xiaoming,Tian, Jie,Zhou, Xiaobo,&Huang, Liyu.(2020).PredictFP2: A New Computational Model to Predict Fusion Peptide Domain in All Retroviruses.IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS,17(5),1714-1720.
MLA Wu, Sijia,et al."PredictFP2: A New Computational Model to Predict Fusion Peptide Domain in All Retroviruses".IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 17.5(2020):1714-1720.

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来源：自动化研究所

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