RNAMotifScan: Automatic Comparing and Searching for RNA Tertiary Motifs using Secondary Structural Alignment

  • Cuncong Zhong, School of EECS, University of Central Florida, Orlando, FL 32816-2362 USA, cczhong at cs dot ucf dot edu
  • Haixu Tang, School of Informatics, Indiana University, Bloomington, IN 47408-3912 USA, htang at indiana dot edu
  • Shaojie Zhang*, School 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.


    Recent studies have shown that RNA tertiary motifs play essential roles in determining RNA folding and functionality. Computational identification and analysis of RNA tertiary motifs remain a challenging task. Existing motif identification methods based on 3D structure may not properly handle motifs with structural variations. Other tertiary motif identification methods consider nested canonical base-pairing structures and cannot be used to identify complex RNA tertiary motifs which often consist of various non-canonical base-pairs due to uncommon hydrogen bond interactions. In this paper, we present a new RNA structure alignment method for RNA tertiary motif identification, which takes into consideration the isosteric (both canonical and non-canonical) base-pairs and multi-pairings in RNA tertiary motifs. Our new method, named RNAMotifScan, aims to find the maximum common isosteric base-pairs between two RNA structures. We tested RNAMotifScan by searching for some previously known RNA strucural motifs within the RNA three dimensional structures from Protein Data Bank (PDB). It is shown that RNAMotifScan has better perfor- mance in terms of both speed and accuracy comparing to current competing methods.

    Please cite the following paper:

    Cuncong Zhong, Haixu Tang, and Shaojie Zhang, "RNAMotifScan: automatic identification of RNA structural motifs using secondary structural alignment", Nucleic Acids Research Aug. 8, 2010.Pubmed Full text
  • Predicted RNA motifs by searching the whole PDB using RNAMotifScan:

    Results in 1S72 is based on FPR cutoff 0.1, instead of p-value cutoff shown in the paper.

  • Kink-turn Motif
  • Kink-turn Motif (non-redundant)
  • Kink-turn Motif (in 1S72, FPR 0.1)
  • C_loop Motif
  • C_loop (non_redundant)
  • C_loop (in 1S72, FPR 0.1)
  • Sarcin-ricin Motif
  • Sarcin-ricin Motif (non-redundant)
  • Sarcin-ricin Motif (in 1S72, FPR 0.1)
  • Reverse Kink turn Motif
  • Reverse Kink turn (non_redundant)
  • Reverse Kink turn (in 1S72, FPR 0.1)
  • E-loop Motif
  • E-loop Motif (non-redundant)
  • E-loop Motif (in 1S72, FPR 0.1)

    Notations in the alignment results:

  • The line labled 'iso' is the isostericity base-pair indication. A Star '*' represents the matched location in the seqeunce is a part of a matched isosteric base-pair. A plus symbol '+' represents the matched location is a part of matched non-isosteric base-pair.
  • The line labeled 'edge' is the interacting edges. 'W' is for Watson-Crick, 'H' is for Hoogsteen, and 'S' is for sugar edge. Upper case letters are for 'cis' orientation base-pairs while lower case letters are for 'trans' orientation base-pairs.
  • The line labeled 'struc' represents the base-pair locations. A pair of '(' and ')' represent the base-pair that was identified in the first stage, while '<' and '>' represent the base-pair that was identified in the second stage.
  • A dot in the sequence represents the breakage location of the original sequence due to presentation of multiple strands in the query motif. An '-' symbol represents a gap in the sequence.

    Comparision of Score Distribution between Real Segments in PDB and Simulated Segments:

  • EPS Figure

    Comparison of E-loop Superimpositions

  • Superimposing Model E-loop (blue) and new found instance (red)
  • Superimposing Model E-loop (blue) and regular A-form helix (green)

    Download RNAMotifScan:

  • Please modify the 6th line in file 'RNAMotifScan.pl' and the 8th line in file 'RNAMotifScan.pm' to specify the directory where the package is located in your workstation. Please also recompile the excutables 'RNAMotifAlign' and 'RNAMotifAlign_align' using commands 'make new' and 'make' before running the program. Sorry for the inconvenience.
  • RNAMotifScan