RASS: a Web Server for RNA Alignment in the Joint Sequence-structure Space

Overview

Journal Nucleic Acids Res

Publisher Oxford University Press

Specialty Biochemistry

Date 2014 May 17

PMID 24831547

Citations 7

Authors

Gewen He

Albert Steppi

Jose Laborde

Anuj Srivastava

Peixiang Zhao

Jinfeng Zhang

Affiliations

Soon will be listed here.

Abstract

Comparison of ribonucleic acid (RNA) molecules is important for revealing their evolutionary relationships, predicting their functions and predicting their structures. Many methods have been developed for comparing RNAs using either sequence or three-dimensional (3D) structure (backbone geometry) information. Sequences and 3D structures contain non-overlapping sets of information that both determine RNA functions. When comparing RNA 3D structures, both types of information need to be taken into account. However, few methods compare RNA structures using both sequence and 3D structure information. Recently, we have developed a new method based on elastic shape analysis (ESA) that compares RNA molecules by combining both sequence and 3D structure information. ESA treats RNA structures as 3D curves with sequence information encoded on additional coordinates so that the alignment can be performed in the joint sequence-structure space. The similarity between two RNA molecules is quantified by a formal distance, geodesic distance. In this study, we implement a web server for the method, called RASS, to make it publicly available to research community. The web server is located at http://cloud.stat.fsu.edu/RASS/.

Citing Articles

LocalSTAR3D: a local stack-based RNA 3D structural alignment tool.

Chen X, Khan N, Zhang S Nucleic Acids Res. 2020; 48(13):e77.

PMID: 32496533 PMC: 7367197. DOI: 10.1093/nar/gkaa453.

RMalign: an RNA structural alignment tool based on a novel scoring function RMscore.

Zheng J, Xie J, Hong X, Liu S BMC Genomics. 2019; 20(1):276.

PMID: 30961545 PMC: 6454663. DOI: 10.1186/s12864-019-5631-3.

SupeRNAlign: a new tool for flexible superposition of homologous RNA structures and inference of accurate structure-based sequence alignments.

Piatkowski P, Jablonska J, Zyla A, Niedzialek D, Matelska D, Jankowska E Nucleic Acids Res. 2017; 45(16):e150.

PMID: 28934487 PMC: 5766185. DOI: 10.1093/nar/gkx631.

iPARTS2: an improved tool for pairwise alignment of RNA tertiary structures, version 2.

Yang C, Shih C, Chen K, Lee P, Tsai P, Lin J Nucleic Acids Res. 2016; 44(W1):W328-32.

PMID: 27185896 PMC: 4987943. DOI: 10.1093/nar/gkw412.

CHSalign: A Web Server That Builds upon Junction-Explorer and RNAJAG for Pairwise Alignment of RNA Secondary Structures with Coaxial Helical Stacking.

Hua L, Song Y, Kim N, Laing C, Wang J, Schlick T PLoS One. 2016; 11(1):e0147097.

PMID: 26789998 PMC: 4720362. DOI: 10.1371/journal.pone.0147097.

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