iDNA6mA-PseKNC: Identifying DNA N6-methyladenosine sites by incorporating nucleotide physicochemical properties into PseKNC

被引：249

作者：

Feng, Pengmian ^{[1
]}

Yang, Hui ^{[2
]}

Ding, Hui ^{[2
]}

Lin, Hao ^{[2
,5
]}

Chen, Wei ^{[3
,4
,5
]}

Chou, Kuo-Chen ^{[2
,5
]}

机构：

[1] North China Univ Sci & Technol, Hebei Prov Key Lab Occupat Hlth & Safety Coal Ind, Sch Publ Hlth, Tangshan 063000, Peoples R China

[2] Univ Elect Sci & Technol China, Key Lab Neuroinformat, Sch Life Sci & Technol, Minist Educ,Ctr Informat Biol, Chengdu 610054, Sichuan, Peoples R China

[3] North China Univ Sci & Technol, Dept Phys, Sch Sci, Tangshan 063000, Peoples R China

[4] North China Univ Sci & Technol, Ctr Genom & Computat Biol, Tangshan 063000, Peoples R China

[5] Gordon Life Sci Inst, Boston, MA 02478 USA

来源：

GENOMICS | 2019年 / 111卷 / 01期

基金：

中国博士后科学基金;

关键词：

PTMs; N-6-methyladenine; Nucleotide physicochemical properties; General PseKNC; Lingering density; Intuitive metrics; AMINO-ACID-COMPOSITION; SEQUENCE-BASED PREDICTOR; MEMBRANE-PROTEIN TYPES; LYSINE SUCCINYLATION SITES; LABEL LEARNING CLASSIFIER; SUPPORT VECTOR MACHINES; SUBCELLULAR-LOCALIZATION; K-TUPLE; RECOMBINATION SPOTS; STRUCTURAL CLASS;

D O I：

10.1016/j.ygeno.2018.01.005

中图分类号：

Q81 [生物工程学（生物技术）]; Q93 [微生物学];

学科分类号：

071005 ; 0836 ; 090102 ; 100705 ;

摘要：

N-6-methyladenine (6mA) is one kind of post-replication modification (PTM or PTRM) occurring in a wide range of DNA sequences. Accurate identification of its sites will be very helpful for revealing the biological functions of 6mA, but it is time-consuming and expensive to determine them by experiments alone. Unfortunately, so far, no bioinformatics tool is available to do so. To fill in such an empty area, we have proposed a novel predictor called iDNA6mA-PseKNC that is established by incorporating nucleotide physicochemical properties into Pseudo K-tuple Nucleotide Composition (PseKNC). It has been observed via rigorous cross-validations that the predictor's sensitivity (Sn), specificity (Sp), accuracy (Acc), and stability (MCC) are 93%, 100%, 96%, and 0.93, respectively. For the convenience of most experimental scientists, a user-friendly web server for iDNA6mA-PseKNC has been established at http://lin-group.cn/server/iDNA6mA-PseKNC, by which users can easily obtain their desired results without the need to go through the complicated mathematical equations involved.

引用

页码：96 / 102

页数：7

共 154 条

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