RNAMotifScanX: a graph alignment approach for RNA structural motif identification

  • Cuncong Zhong, Department of EECS, University of Central Florida, Orlando, FL 32816-2362 USA, cczhong at cs dot ucf dot edu
  • Shaojie Zhang*, Department of EECS, University of Central Florida, Orlando, FL 32816-2362 USA, shzhang at cs dot ucf dot edu
  • *To whom correspondence should be addressed to.

    Abstract

    RNA structural motifs are recurrent three-dimensional (3D) components found in the RNA architecture. These RNA structural motifs play important structural or functional roles and usually exhibit highly conserved 3D geometries and base-interaction patterns. Analysis of the RNA 3D structures and elucidation of their molecular functions heavily rely on efficient and accurate identification of these motifs. However, efficient RNA structural motif search tools are lacking due to the high complexity of these motifs. In this work we present RNAMotifScanX, a motif search tool based on a base-interaction graph alignment algorithm. This novel algorithm enables automatic identification of both partially and fully matched motif instances. RNAMotifScanX considers non-canonical base-pairing interactions, base-stacking interactions, and sequence conservation of the motifs, which leads to significantly improved sensitivity and specificity as compared to other state-of-the-art search tools. RNAMotifScanX also adopts a carefully designed branch-and-bound technique, which enables ultra-fast search of large kink-turn motifs against a 23S rRNA. The software package RNAMotifScanX is implemented using GNU C++.

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    The following executables of RNAMotifScanX were compiled with Linux 64-bit system. For source code please contact the authors.
  • RNAMotifScanX-release_v0.0.5_x86-64_rhel.tar.gz

    Download Prebuilt PDB annotation files: (last update: Mar. 10th, 2015)

  • Prebuilt PDB files (individual structures)
  • Prebuilt PDB files (.tgz archive of all structures)

    Citation

    If you find RNAMotifScanX useful, please kindely cite:
  • Zhong. C and Zhang. S, RNAMotifScanX: a graph alignment approach for RNA structural motif identification, RNA. 2015 Mar;21(3):333-46. doi: 10.1261/rna.044891.114. Epub 2015 Jan 16.

    • Comments or Questions?

    Please contact Cuncong Zhong through email cczhong at eecs.ucf.edu