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• W2883467144 abstract "Abstract Motivation Identification of DNA-binding proteins from only sequence information is one of the most challenging problems in the field of genome annotation. DNA-binding proteins play an important role in various biological processes such as DNA replication, repair, transcription and splicing. Existing experimental techniques for identifying DNA-binding proteins are time-consuming and expensive. Thus, prediction of DNA-binding proteins from sequences alone using computational methods can be useful to quickly annotate and guide the experimental process. Most of the methods developed for predicting DNA-binding proteins use the information from the evolutionary profile, called the position-specific scoring matrix (PSSM) profile, alone and the accuracies of such methods have been limited. Here, we propose a method, called StackDPPred, which utilizes features extracted from PSSM and residue specific contact-energy to help train a stacking based machine learning method for the effective prediction of DNA-binding proteins. Results Based on benchmark sequences of 1063 (518 DNA-binding and 545 non DNA-binding) proteins and using jackknife validation, StackDPPred achieved an ACC of 89.96%, MCC of 0.799 and AUC of 94.50%. This outcome outperforms several state-of-the-art approaches. Furthermore, when tested on recently designed two independent test datasets, StackDPPred outperforms existing approaches consistently. The proposed StackDPPred can be used for effective prediction of DNA-binding proteins from sequence alone. Availability and implementation Online server is at http://bmll.cs.uno.edu/add and code-data is at http://cs.uno.edu/∼tamjid/Software/StackDPPred/code_data.zip. Supplementary information Supplementary data are available at Bioinformatics online." @default.
• W2883467144 created "2018-08-03" @default.
• W2883467144 creator A5022045445 @default.
• W2883467144 creator A5032814089 @default.
• W2883467144 creator A5055092646 @default.
• W2883467144 date "2018-07-19" @default.
• W2883467144 modified "2023-10-06" @default.
• W2883467144 title "StackDPPred: a stacking based prediction of DNA-binding protein from sequence" @default.
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• W2883467144 doi "https://doi.org/10.1093/bioinformatics/bty653" @default.
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