Star3D: A Stack-Based Rna 3D Structural Alignment Tool

Abstract

The various roles of versatile non-coding RNAs typically require the attainment of complex high-order structures. Therefore, comparing the 3D structures of RNA molecules can yield in-depth understanding of their functional conservation and evolutionary history. Recently, many powerful tools have been developed to align RNA 3D structures. Although some methods rely on both backbone conformations and base pairing interactions, none of them consider the entire hierarchical formation of the RNA secondary structure. One of the major issues is that directly applying the algorithms of matching 2D structures to the 3D coordinates is particularly time-consuming. In this article, we propose a novel RNA 3D structural alignment tool, STAR3D, to take into full account the 2D relations between stacks without the complicated comparison of secondary structures. First, the 3D conserved stacks in the inputs are identified and then combined into a tree-like consensus. Afterward, the loop regions are compared one-to-one in accordance with their relative positions in the consensus tree. The experimental results show that the prediction of STAR3D is more accurate for both non-homologous and homologous RNAs than other state-of-the-art tools with shorter running time.

Publication Date

6-26-2015

Publication Title

Nucleic Acids Research

Volume

43

Issue

20

Document Type

Article

Personal Identifier

scopus

DOI Link

https://doi.org/10.1093/nar/gkv697

Socpus ID

84950156157 (Scopus)

Source API URL

https://api.elsevier.com/content/abstract/scopus_id/84950156157

This document is currently not available here.

Share

COinS