Abstract

Understanding the fine details of the 3D structure will play a critical role in identifying RNA functional characteristics and designing new RNAs for RNA-based therapeutics and nanotechnology. While several existing computational methods can help in finding similar structural components in RNAs to some extent, they do not provide the means to compare and contrast those components extensively. We have developed a new method, RNAMotifContrast, which can help to visualize and analyze significant features of RNA structural motifs (a key component in RNA architecture and functions) and their relations more closely to achieve valuable insight into RNA's diverse roles. We have applied this method on a dataset of known RNA structural motif instances and assessed its effectiveness. With the analysis of similarities and variations, we have identified subfamilies of RNA structural motifs for the first time. The subfamilies possess unique variations of structural features while holding common features of the families. The outcome of our work provides a new perspective of RNA structural motifs and shows the potential of our method to aid in further research on different datasets and analyze various aspects of RNA structures and functions.

• Shahidul Islam, Department Computer Science, University of Central Florida, Orlando, FL 32816 USA, shahidul at knights dot ucf dot edu
• Md Mahfuzur Rahaman, Department Computer Science, University of Central Florida, Orlando, FL 32816 USA, mahfuzur at knights dot ucf dot edu
• Shaojie Zhang*, Department Computer Science, University of Central Florida, Orlando, FL 32816 USA, shzhang at cs dot ucf dot edu

*To whom correspondence should be addressed to.