Identification of DNA-binding proteins using multi-features fusion and binary firefly optimization algorithm

BMC Bioinformatics

Research Article

Bo Gao¹  Haiting Chai¹  Jian Zhang¹  Zhiqiang Ma¹  Guifu Yang² 

[1]School of Computer Science and Information Technology, Northeast Normal University, 130117, Changchun, People’s Republic of China

[2]School of Computer Science and Information Technology, Northeast Normal University, 130117, Changchun, People’s Republic of China

[3]Office of Informatization Management and Planning, Northeast Normal University, 130117, Changchun, People’s Republic of China

关键词: DNA-binding proteins;    Binary firefly algorithm;    Feature selection;    Parameters optimization;   

DOI  :  10.1186/s12859-016-1201-8

 received in 2016-01-21, accepted in 2016-08-24,  发布年份 2016

来源: Springer

【 摘 要 】

BackgroundDNA-binding proteins (DBPs) play fundamental roles in many biological processes. Therefore, the developing of effective computational tools for identifying DBPs is becoming highly desirable.ResultsIn this study, we proposed an accurate method for the prediction of DBPs. Firstly, we focused on the challenge of improving DBP prediction accuracy with information solely from the sequence. Secondly, we used multiple informative features to encode the protein. These features included evolutionary conservation profile, secondary structure motifs, and physicochemical properties. Thirdly, we introduced a novel improved Binary Firefly Algorithm (BFA) to remove redundant or noisy features as well as select optimal parameters for the classifier. The experimental results of our predictor on two benchmark datasets outperformed many state-of-the-art predictors, which revealed the effectiveness of our method. The promising prediction performance on a new-compiled independent testing dataset from PDB and a large-scale dataset from UniProt proved the good generalization ability of our method. In addition, the BFA forged in this research would be of great potential in practical applications in optimization fields, especially in feature selection problems.ConclusionsA highly accurate method was proposed for the identification of DBPs. A user-friendly web-server named iDbP (identification of DNA-binding Proteins) was constructed and provided for academic use.

【 授权许可】

CC BY   
© The Author(s). 2016

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