scholarly journals SETTER: web server for RNA structure comparison

2012 ◽  
Vol 40 (W1) ◽  
pp. W42-W48 ◽  
Author(s):  
Petr Čech ◽  
Daniel Svozil ◽  
David Hoksza
Keyword(s):  
Rna Structure ◽  
Web Server ◽  
Structure Comparison

scholarly journals MultiSETTER: web server for multiple RNA structure comparison

2015 ◽  
Vol 16 (1) ◽  
Author(s):  
Petr Čech ◽  
David Hoksza ◽  
Daniel Svozil
Keyword(s):  
Rna Structure ◽  
Web Server ◽  
Structure Comparison

scholarly journals RNATOPS-W: a web server for RNA structure searches of genomes

2009 ◽  
Vol 25 (8) ◽  
pp. 1080-1081 ◽  
Author(s):  
Yingfeng Wang ◽  
Zhibin Huang ◽  
Yong Wu ◽  
Russell L. Malmberg ◽  
Liming Cai
Keyword(s):  
Rna Structure ◽  
Web Server

scholarly journals TRFolder-W: a web server for telomerase RNA structure prediction in yeast genomes

2012 ◽  
Vol 28 (20) ◽  
pp. 2696-2697
Author(s):  
D. Zhang ◽  
X. Xue ◽  
R. L. Malmberg ◽  
L. Cai
Keyword(s):  
Rna Structure ◽  
Structure Prediction ◽  
Web Server ◽  
Telomerase Rna ◽  
Rna Structure Prediction ◽  
Yeast Genomes

scholarly journals MutaRNA: analysis and visualization of mutation-induced changes in RNA structure

2020 ◽  
Vol 48 (W1) ◽  
pp. W287-W291
Author(s):  
Milad Miladi ◽  
Martin Raden ◽  
Sven Diederichs ◽  
Rolf Backofen
Keyword(s):  
Rna Structure ◽  
Web Server ◽  
Regulatory Elements ◽  
Intramolecular Interactions ◽  
Messenger Rnas ◽  
Base Pairing ◽  
Single Nucleotide Variants ◽  
Single Nucleotide ◽  
Induced Changes ◽  
The Impact

Abstract RNA molecules fold into complex structures as a result of intramolecular interactions between their nucleotides. The function of many non-coding RNAs and some cis-regulatory elements of messenger RNAs highly depends on their fold. Single-nucleotide variants (SNVs) and other types of mutations can disrupt the native function of an RNA element by altering its base pairing pattern. Identifying the effect of a mutation on an RNA’s structure is, therefore, a crucial step in evaluating the impact of mutations on the post-transcriptional regulation and function of RNAs within the cell. Even though a single nucleotide variation can have striking impacts on the structure formation, interpreting and comparing the impact usually needs expertise and meticulous efforts. Here, we present MutaRNA, a web server for visualization and interpretation of mutation-induced changes on the RNA structure in an intuitive and integrative fashion. To this end, probabilities of base pairing and position-wise unpaired probabilities of wildtype and mutated RNA sequences are computed and compared. Differential heatmap-like dot plot representations in combination with circular plots and arc diagrams help to identify local structure abberations, which are otherwise hidden in standard outputs. Eventually, MutaRNA provides a comprehensive and comparative overview of the mutation-induced changes in base pairing potentials and accessibility. The MutaRNA web server is freely available at http://rna.informatik.uni-freiburg.de/MutaRNA.

Efficient RNA structure comparison algorithms

2017 ◽  
Vol 15 (06) ◽  
pp. 1740009 ◽  
Author(s):  
Abdullah N. Arslan ◽  
Jithendar Anandan ◽  
Eric Fry ◽  
Keith Monschke ◽  
Nitin Ganneboina ◽  
...  
Keyword(s):  
Rna Structure ◽  
Search Algorithm ◽  
Suffix Array ◽  
Rna Structures ◽  
Structure Comparison ◽  
Structure Representation ◽  
Substructure Search ◽  
Common Substructure ◽  
Search Tool ◽  
Comparison Algorithms

Recently proposed relative addressing-based ([Formula: see text]) RNA secondary structure representation has important features by which an RNA structure database can be stored into a suffix array. A fast substructure search algorithm has been proposed based on binary search on this suffix array. Using this substructure search algorithm, we present a fast algorithm that finds the largest common substructure of given multiple RNA structures in [Formula: see text] format. The multiple RNA structure comparison problem is NP-hard in its general formulation. We introduced a new problem for comparing multiple RNA structures. This problem has more strict similarity definition and objective, and we propose an algorithm that solves this problem efficiently. We also develop another comparison algorithm that iteratively calls this algorithm to locate nonoverlapping large common substructures in compared RNAs. With the new resulting tools, we improved the RNASSAC website (linked from http://faculty.tamuc.edu/aarslan ). This website now also includes two drawing tools: one specialized for preparing RNA substructures that can be used as input by the search tool, and another one for automatically drawing the entire RNA structure from a given structure sequence.

scholarly journals Vfold: A Web Server for RNA Structure and Folding Thermodynamics Prediction

PLoS ONE ◽  
2014 ◽  
Vol 9 (9) ◽  
pp. e107504 ◽  
Author(s):  
Xiaojun Xu ◽  
Peinan Zhao ◽  
Shi-Jie Chen
Keyword(s):  
Rna Structure ◽  
Web Server ◽  
Folding Thermodynamics

scholarly journals SHAPER: A Web Server for Fast and Accurate SHAPE Reactivity Prediction

2021 ◽  
Vol 8 ◽  
Author(s):  
Yuanzhe Zhou ◽  
Jun Li ◽  
Travis Hurst ◽  
Shi-Jie Chen
Keyword(s):  
Rna Structure ◽  
Structural Information ◽  
3D Structure ◽  
Web Server ◽  
Rna Structures ◽  
Structure Selection ◽  
Chemical Probing ◽  
Local Flexibility ◽  
Multiple Conformations ◽  
Shape Data

Selective 2′-hydroxyl acylation analyzed by primer extension (SHAPE) chemical probing serves as a convenient and efficient experiment technique for providing information about RNA local flexibility. The local structural information contained in SHAPE reactivity data can be used as constraints in 2D/3D structure predictions. Here, we present SHAPE predictoR (SHAPER), a web server for fast and accurate SHAPE reactivity prediction. The main purpose of the SHAPER web server is to provide a portal that uses experimental SHAPE data to refine 2D/3D RNA structure selection. Input structures for the SHAPER server can be obtained through experimental or computational modeling. The SHAPER server can accept RNA structures with single or multiple conformations, and the predicted SHAPE profile and correlation with experimental SHAPE data (if provided) for each conformation can be freely downloaded through the web portal. The SHAPER web server is available at http://rna.physics.missouri.edu/shaper/.

scholarly journals Estimating the power of sequence covariation for detecting conserved RNA structure

2020 ◽  
Vol 36 (10) ◽  
pp. 3072-3076 ◽  
Author(s):  
Elena Rivas ◽  
Jody Clements ◽  
Sean R Eddy
Keyword(s):  
Secondary Structure ◽  
Sequence Alignment ◽  
Rna Structure ◽  
Rna Secondary Structure ◽  
Source Code ◽  
Web Server ◽  
Supplementary Information ◽  
Supplementary Data ◽  
Detection Power ◽  
Non Coding Rnas

Abstract Pairwise sequence covariations are a signal of conserved RNA secondary structure. We describe a method for distinguishing when lack of covariation signal can be taken as evidence against a conserved RNA structure, as opposed to when a sequence alignment merely has insufficient variation to detect covariations. We find that alignments for several long non-coding RNAs previously shown to lack covariation support do have adequate covariation detection power, providing additional evidence against their proposed conserved structures. Availability and implementation The R-scape web server is at eddylab.org/R-scape, with a link to download the source code. Supplementary information Supplementary data are available at Bioinformatics online.

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