Depth-First Search Encoding of RNA Substructures

  • Qingfeng Chen
  • 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)

Abstract

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.

Keywords

Data mining RNA Subgraph Substructure Support 

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Copyright information

© Springer International Publishing Switzerland 2016

Authors and Affiliations

  • Qingfeng Chen
    • 1
    • 2
  • 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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