Comparison of Similar RNA 3D Structures and Substructures Search Tools

Abstract

ncRNAs functions in the cells has produced exponentially increasing data of RNA 3D structures in both PDB and NDB. Tools are needed to search for similar RNA 3D structures in hope to aid with annotation processes. In this article, five tools (ARTS, FASTR3D, RNA FRABASE 2.0, RAG-3D, and R3D-BLAST2) will be compared based on their performances in analyzing samples of RNA 3D structures in different sizes (pseudoknot, 5S rRNA, and 18S rRNA). ARTS was found to be the most outdated and slow tools, while FASTR3D and RNA FRABASE 2.0 is commonly used as a benchmarking standard. RAG-3D & R3D-BLAST2 produces results with the highest accuracy and is still relevant in the present, however, RAG-3D is found to be limited to analyze RNA 3D structures to a certain size (it cannot process very large samples). This article also provides suggestion for future studies to create tools with similar purposes.