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iN6-methylat (5-step): identifying DNA N6-methyladenine sites in rice genome using continuous bag of nucleobases via Chou’s 5-step rule

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  • معلومة اضافية
    • بيانات النشر:
      Springer Science and Business Media LLC, 2019.
    • الموضوع:
      2019
    • نبذة مختصرة :
      DNA N6-methyladenine is a non-canonical DNA modification that occurs in different eukaryotes at low levels and it has been identified as an extremely important function of life. Moreover, about 0.2% of adenines are marked by DNA N6-methyladenine in the rice genome, higher than in most of the other species. Therefore, the identification of them has become a very important area of study, especially in biological research. Despite the few computational tools employed to address this problem, there still requires a lot of efforts to improve their performance results. In this study, we treat DNA sequences by the continuous bags of nucleobases, including sub-word information of its biological words, which then serve as features to be fed into a support vector machine algorithm to identify them. Our model which uses this hybrid approach could identify DNA N6-methyladenine sites with achieved a jackknife test sensitivity of 86.48%, specificity of 89.09%, accuracy of 87.78%, and MCC of 0.756. Compared to the state-of-the-art predictor as well as the other methods, our proposed model is able to yield superior performance in all the metrics. Moreover, this study provides a basis for further research that can enrich a field of applying natural language-processing techniques in biological sequences.
    • ISSN:
      1617-4623
      1617-4615
    • الرقم المعرف:
      10.1007/s00438-019-01570-y
    • Rights:
      CLOSED
    • الرقم المعرف:
      edsair.doi...........2bbff0970a4c938e14736e41dcd1f801