Rsite: a computational method to identify the functional sites of noncoding RNAs

Scientific Reports
Pan ZengQinghua Cui

Abstract

There is an increasing demand for identifying the functional sites of noncoding RNAs (ncRNAs). Here we introduce a tertiary-structure based computational approach, Rsite, which first calculates the Euclidean distances between each nucleotide and all the other nucleotides in a RNA molecule and then determines the nucleotides that are the extreme points in the distance curve as the functional sites. By analyzing two ncRNAs, tRNA (Lys) and Diels-Alder ribozyme, we demonstrated the efficiency of Rsite. As a result, Rsite recognized all of the known functional sites of the two ncRNAs, suggesting that Rsite could be a potentially useful tool for discovering the functional sites of ncRNAs. The source codes and data sets of Rsite are available at http://www.cuilab.cn/rsite.

References

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Citations

May 3, 2018·Bioinformatics·Kaili WangYunjie Zhao
Jun 19, 2021·ACS Medicinal Chemistry Letters·Jingru Xie, Aaron T Frank
Jun 18, 2021·Computational and Structural Biotechnology Journal·Huiwen Wang, Yunjie Zhao
Nov 1, 2021·Drug Discovery Today·Yuyu FengSheng-You Huang

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Methods Mentioned

BETA
footprinting

Software Mentioned

Rsite

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