Xu W., Wongsa A., Lee J., Shang L., Cannone J.J., and Gutell R.R. (2011). RNA2DMap: A Visual Exploration Tool of the Information in RNA's Higher-Order Structure. Proceedings of 2011 IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2011), Atlanta, GA. November 12-15, 2011. IEEE Computer Society, Washington, DC, USA. pp. 613-617.

1. RNA2DMap: A Visual Exploration Tool of the Information in RNA’s Higher-
Order Structure
Weijia Xu1,†
Ame Wongsa 2, ‡
Jung Lee 3,
*
Lei Shang4,
* Jamie J Cannone 5,
* Robin R. Gutell 6,
*
†
Texas Advanced Computing Center,
‡
School of Information, *Institute for Cellular and Molecular Biology
The University of Texas at Austin
Austin, Texas, USA
1
xwj@tacc.utexas.edu; 2
Amewongsa@gmail.com; 3
bojungx@gmail.com;
4
leishang@mail.utexas.edu;
5
jjcannone@austin.utexas.edu;
6
robin.gutell@mail.utexas.edu;
Abstract -- A new and emerging paradigm in molecular biology
is revealing that RNA is implicated in nearly every aspect of
the metabolism in the cell. To enhance our understanding of
the function of these RNA molecules in the cell, it is essential
that we have a complete understanding of their higher-order
structures. While many computational tools have been
developed to predict and analyse these higher-order RNA
structures, few are able to visualize them for analytical
purposes. In this paper, we present an interactive visualization
tool of the secondary structure of RNA, named RNA2DMap.
This program enables multiple-dimensions of information
about RNA structure to be selected, customized and displayed
to visually identify patterns and relationships. RNA2DMap
facilitates the comparative analysis and understanding of
RNAs that cannot be readily obtained with other graphical or
text output from computer programs. Three use cases are
presented to illustrate how RNA2DMap aids structural
analysis.
Keywords: Biological Data Visulation; RNA Struaral Analysis;
Interative Application
I. INTRODUCTION
RNA structure, function, and evolution are studied with
experimental and computational methods. Comparative
analysis, one of the computational methods, has been used
to determine an RNA’s higher-order structure with high
accuracy and detail, principles of RNA structure, and the
evolution of RNA and phylogenetic relationships. This
analysis is dependent on the number and diversity of the
RNA sequences and high-resolution crystal structures
within any given RNA family, and the sophistication of the
computational system to analyse the data. Information
related to RNA sequences is usually stored within a
database or in text files with specific formats. We have
developed rCAD – RNA Comparative Analysis Database
that utilizes the Microsoft SQL-server to organize,
manipulate, and analyse these multiple dimensions of
information [1] [2]. rCAD is the foundation used to
effectively create inter-relationships between multiple types
of information. However, from these patterns, biases and
relationships in rCAD’s data, we are unable to synthesize all
of this knowledge into a complete understanding of RNA’s
structure, function, and evolution..
While most computational approaches are developed
based on data mining and algorithmic approaches to
understand the structure and functions of RNA molecules,
visual analytic approaches can provide insights from the
data. The secondary structure diagram of RNA is routinely
used to visualize the base pairs, helices, and structural
motifs of the RNA’s higher-order structure. It is the
reference point for discussion and analysis of sequence
alignments, high-resolution crystal structures, and
evolutionary relationships. Many RNA scientists map their
experimental data and other relevant information onto these
diagrams. However this is usually done on a figure in a
published paper, not as an interactive graphics display.
Our goal is to create a new and novel application to allow
researchers to dynamically navigate through this myriad of
multiple dimensions of information. RNA2DMap, the focus
of this paper, is a new foundation for the dynamic visual
presentation of the growing number of data types that will
enhance our knowledge of RNA structure, folding, and its
evolution. RNA2DMap is akin to the Macroscope, an
abstract computational system to facilitate an understanding
of a complex system from all of its components, both
physical and temporal. RNA2DMap is available at
http://www.rna.ccbb.utexas.edu/SAE/2A/RNA2DMap/inde
x.php, part of Comparative RNA Web (CRW) Site [3].
II. BACKGROUND AND RELATED WORK
The initial attempts to visualize RNA secondary
structure focused on the automatic drawing algorithms to
generate aesthetically pleasing secondary structure diagrams
with very limited overlap of strands and interactions [4] [5]
[6]. A radial drawing algorithm was implemented in
RNAViz which draws each helix and base in a multi-loop at
regular angular distances [7]. JViz, includes multiple
drawing algorithms such as linear linked graph [8], circular
representation and RNA dot plot [9]. RNAView is one of
the first applications that displays the tertiary interactions
with RNA secondary structure [10]. PseudoViewer is a tool
for visualizing RNA secondary structure with Pseudoknots,
a special type of structure motifs. PseudoViewer can
efficiently visualize a large RNA sequence with any type of
pseudoknot as a compact planar drawing. PseudoViewer
claims to be 10 times faster than the previous algorithm and
produces a more aesthetic structure [11].
Recent developments add features such as interactive
editing, annotation, and comparison among a set of RNA
2011 IEEE International Conference on Bioinformatics and Biomedicine
978-0-7695-4574-5/11 $26.00 © 2011 IEEE
DOI 10.1109/BIBM.2011.60
613

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them from
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nucleotide
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[26]. Our
l regions of
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A2DMap to
sed on the
re of the T.
eotides are
that these
616

5. nucleotides might form a base pair or are sufficiently close
in three-dimensional space to have structural constraints
with the other nucleotides in these clusters of neighbour
effects. This observation with RNA2DMap increases our
confidence that these neighbour effects are true structural
constraints and demonstrates nucleotides that do not form a
base pair can influence the evolution of other nucleotides
that are physically close with one another.
V. CONCLUSIONS
In this paper, we present RNA2DMap, an interactive tool
for visualizing multiple types of information on an RNA
secondary structure. The primary visualization is based on
the standard RNA secondary structure diagram. Nested
circles with different colors were used to reveal multiple
dimensions of information, including base pair types, base
pair conformations, conservation values of RNA sequences,
and the physical three-dimensional distances between the
selected nucleotide and all other nucleotides. RNA2DMap
has the flexibility to show different combinations of
information on the RNA secondary structure. We
demonstrate three use cases. The first reveals the frequency
and organization of the different base pair types and their
conformations. The second reveals tertiary interactions
associated with a few of the structural motifs. The third
utilizes the RNA distance function to determine if different
sets of positions with a weak covariation are sufficiently
close in three-dimensional space to either form a base pair
or affect the spatial constraints of the nucleotides on other
nucleotides in this local region of the RNA structure.
RNA2DMap can be adapted to work with any secondary
structure diagram generated with other programs.
ACKNOWLEDGEMENT
This work was supported by NIH grants GM085337
(awarded to RG and WX) and GM067317 (awarded to RG),
and the Welch Foundation F-1427 (awarded to RG).
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