SARSA: a Web Tool for Structural Alignment of RNA Using a Structural Alphabet

Overview

Journal Nucleic Acids Res

Publisher Oxford University Press

Specialty Biochemistry

Date 2008 May 27

PMID 18502774

Citations 20

Authors

Yen-Fu Chang

Yen-Lin Huang

Chin Lung Lu

Affiliations

Soon will be listed here.

Abstract

SARSA is a web tool that can be used to align two or more RNA tertiary structures. The basic idea behind SARSA is that we use the vector quantization approach to derive a structural alphabet (SA) of 23 nucleotide conformations, via which we transform RNA 3D structures into 1D sequences of SA letters and then utilize classical sequence alignment methods to compare these 1D SA-encoded sequences and determine their structural similarities. In SARSA, we provide two RNA structural alignment tools, PARTS for pairwise alignment of RNA tertiary structures and MARTS for multiple alignment of RNA tertiary structures. Particularly in PARTS, we have implemented four kinds of pairwise alignments for a variety of practical applications: (i) global alignment for comparing whole structural similarity, (ii) semiglobal alignment for detecting structural motifs, (iii) local alignment for finding locally similar substructures and (iv) normalized local alignment for eliminating the mosaic effect of local alignment. Both tools in SARSA take as input RNA 3D structures in the PDB format and in their outputs provide graphical display that allows the user to visually view, rotate and enlarge the superposition of aligned RNA molecules. SARSA is available online at http://bioalgorithm.life.nctu.edu.tw/SARSA/.

Citing Articles

A comprehensive survey of long-range tertiary interactions and motifs in non-coding RNA structures.

Bohdan D, Voronina V, Bujnicki J, Baulin E Nucleic Acids Res. 2023; 51(16):8367-8382.

PMID: 37471030 PMC: 10484739. DOI: 10.1093/nar/gkad605.

CircularSTAR3D: a stack-based RNA 3D structural alignment tool for circular matching.

Chen X, Zhang S Nucleic Acids Res. 2023; 51(9):e53.

PMID: 36987885 PMC: 10201423. DOI: 10.1093/nar/gkad222.

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.

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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