期刊
IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS
卷 16, 期 4, 页码 1316-1321出版社
IEEE COMPUTER SOC
DOI: 10.1109/TCBB.2017.2666141
关键词
Prokaryote; sigma70 promoter; PseZNC; multi-window Z-curve; local DNA structural property
类别
资金
- Applied Basic Research Program of Sichuan Province [2015JY0100, 14JC0121]
- Fundamental Research Funds for the Central Universities of China [ZYGX2015J144, ZYGX2015Z006]
- Program for the Top Young Innovative Talents of Higher Learning Institutions of Hebei Province [BJ2014028]
- Outstanding Youth Foundation of North China University of Science and Technology [JP201502]
- China Postdoctoral Science Foundation [2015M582533]
- Scientific Research Foundation of the Education Department of the Sichuan Province [11ZB122]
Promoters are DNA regulatory elements located directly upstream or at the 5' end of the transcription initiation site (TSS), which are in charge of gene transcription initiation. With the completion of a large number of microorganism genomics, it is urgent to predict promoters accurately in bacteria by using the computational method. In this work, a sequence-based predictor named iPro70-PseZNC was designed for identifying sigma70 promoters in prokaryote. In the predictor, the samples of DNA sequences are formulated by a novel pseudo nucleotide composition, called PseZNC, into which the multi-window Z-curve composition and six local DNA structural properties are incorporated. In the 5-fold cross-validation, the area under the curve of receiver operating characteristic of 0.909 was obtained on our benchmark dataset, indicating that the proposed predictor is promising and will provide an important guide in this area. Further studies showed that the performance of PseZNC is better than it of multi-window Z-curve composition. For the sake of convenience for researchers, a user-friendly online service was established and can be freely accessible at http://lin.uestc.edu.cn/server/iPro70-PseZNC. The PseZNC approach can be also extended to other DNA-related problems.
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