Depth-First Search Encoding of RNA Substructures

  • Qingfeng ChenEmail author
  • Chaowang Lan
  • Jinyan Li
  • Baoshan Chen
  • Lusheng Wang
  • Chengqi Zhang
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 9771)


RNA structural motifs are important in RNA folding process. Traditional index-based and shape-based schemas are useful in modeling RNA secondary structures but ignore the structural discrepancy of individual RNA family member. Further, the in-depth analysis of underlying substructure pattern is underdeveloped owing to varied and unnormalized substructures. This prevents us from understanding RNAs functions. This article proposes a DFS (depth-first search) encoding for RNA substructures. The results show that our methods are useful in modelling complex RNA secondary structures.


Data mining RNA Subgraph Substructure Support 



The work reported in this paper was partially supported by two National Natural Science Foundation of China projects 61363025 and 61373048, two key projects of Natural Science Foundation of Guangxi 2012GXNSFCB053006 and 2013GXNSFDA019029, and a grant from the Research Grants Council of the Hong Kong Special Administrative Region, [Project No. CityU 123013].


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Copyright information

© Springer International Publishing Switzerland 2016

Authors and Affiliations

  • Qingfeng Chen
    • 1
    • 2
    Email author
  • Chaowang Lan
    • 1
  • Jinyan Li
    • 3
  • Baoshan Chen
    • 2
  • Lusheng Wang
    • 4
  • Chengqi Zhang
    • 5
  1. 1.School of Computer, Electronic and InformationGuangxi UniversityNanningChina
  2. 2.State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresourcesGuangxi UniversityNanningChina
  3. 3.Advanced Analytics InstituteUniversity of Technology SydneyUltimoAustralia
  4. 4.Department of Computer ScienceCity University of Hong KongKowloonHong Kong
  5. 5.Centre for Quantum Computation and Intelligent SystemsUniversity of Technology SydneyUltimoAustralia

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