RSmatch 2.0 – Comparison of RNA structures

RSmatch 2.0

:: DESCRIPTION

RSmatch is a package for comparing RNA structures via 1) pair-wise and DB searches; 2) multiple structure alignment with common structure computation; 3)iterative DB searches.

::DEVELOPER

Shapiro Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows

:: DOWNLOAD

RSmatch

Khaladkar M, Bellofatto V, Wang JT, Tian B, Shapiro BA.
RADAR: a web server for RNA data analysis and research.
Nucleic Acids Res. 2007 Jul;35(Web Server issue):W300-4. doi: 10.1093/nar/gkm253. Epub 2007 May 21. PMID: 17517784; PMCID: PMC1933136.

Vfold 2.0 – RNA Structure and Folding Thermodynamics Prediction

Vfold 2.0

:: DESCRIPTION

Vfold is a software package to evaluate the stable structures and the folding free energies for RNA secondary structures and pseudoknotted structures. Recently, the Vfold model has been extended to predict loop-stem tertiary interactions in RNA pseudoknots

::DEVELOPER

Shi-Jie Chen Research Group

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Linux

:: DOWNLOAD

 Vfold

:: MORE INFORMATION

Citation

Vfold: a web server for RNA structure and folding thermodynamics prediction.
Xu X, Zhao P, Chen SJ.
PLoS One. 2014 Sep 12;9(9):e107504. doi: 10.1371/journal.pone.0107504. eCollection 2014.

PRI-Modeler 1.3 – Extract RNA Structure elements from PDB files of Protein-RNA Complexes

PRI-Modeler 1.3

:: DESCRIPTION

PRI-Modeler (protein-RNA interaction modeler)analyzes the conformation of the RNA, calculates the hydrogen bond (H bond) and van der Waals interactions between amino acids and nucleotides, extracts secondary and tertiary RNA structure elements, and identifies the patterns of interactions between the proteins and RNAs. This paper presents PRI-Modeler and its application to the hydrogen bond and van der Waals interactions in the most representative set of protein-RNA complexes. The analysis reveals several interesting interaction patterns at various levels.

::DEVELOPER

Biocomputing Lab. School of Computer Science and Engineering Inha University, Inchon

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

PRI-Modeler

:: MORE INFORMATION

Citation

Kyungsook Han, Chirag Nepa
PRI-Modeler: Extracting RNA structural elements from PDB files of protein–RNA complexes
FEBS Lett. 2007 May 1;581(9):1881-90.

Gardenia – Compare & Align RNA Structures

Gardenia

:: DESCRIPTION

Gardenia is a program that Compares & aligns RNA secondary structures,without pseudoknots. The resulting alignment takes into account both the primary structure and the secondary structure.

::DEVELOPER

Bonsai Bioinformatics – INRIA

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows /  Linux / MacOsX
  • C Complier

:: DOWNLOAD

Gardenia

:: MORE INFORMATION

Citation

Guillaume Blin, Alain Denise, Serge Dulucq, Claire Herrbach, Helene Touzet
Alignment of RNA structures
IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2008

RNAsnp 1.2 – Identifying local RNA Structures Disrupted by SNPs

RNAsnp 1.2

:: DESCRIPTION

RNAsnp is a software for efficient detection of local RNA secondary structure changes induced by SNPs

::DEVELOPER

Center for non-coding RNA in Technology and Health (RTH)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

  RNAsnp

:: MORE INFORMATION

Citation:

Hum Mutat. 2013 Apr;34(4):546-56. doi: 10.1002/humu.22273.
RNAsnp: efficient detection of local RNA secondary structure changes induced by SNPs.
Sabarinathan R, Tafer H, Seemann SE, Hofacker IL, Stadler PF, Gorodkin J.

SAVoR – Sequencing Annotation and Visualization of RNA structures

SAVoR

:: DESCRIPTION

SAVoR is an easy-to-use web application that allows the user to visualize RNA-seq data and other genomic annotations on RNA secondary structures. SAVoR is designed to help researchers visualize sequencing data in the context of RNA secondary structures.

::DEVELOPER

 Wang Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

  NO

:: MORE INFORMATION

Citation

SAVoR: a server for sequencing annotation and visualization of RNA structures.
Li F, Ryvkin P, Childress DM, Valladares O, Gregory BD, Wang LS.
Nucleic Acids Res. 2012 Jul;40(Web Server issue):W59-64. doi: 10.1093/nar/gks310.

CARNA 1.3.3 – Alignment of RNA Structure Ensembles

CARNA 1.3.3

:: DESCRIPTION

CARNA is a tool for multiple alignment of RNA molecules. CARNA requires only the RNA sequences as input and will compute base pair probability matrices and align the sequences based on their full ensembles of structures.

::DEVELOPER

Chair for Bioinformatics Freiburg

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Dragos A. Sorescu, Mathias Moehl, Martin Mann, Rolf Backofen, and Sebastian Will
CARNA – alignment of RNA structure ensembles
Nucleic Acids Reseach, 40 no. W1 pp. W49-W53, 2012

ProbRNA 20131213 – Modeling RNA Structure Probing data

ProbRNA 20131213

:: DESCRIPTION

ProbRNA produces features found to be related to both the secondary and tertiary structures of the RNAs.

::DEVELOPER

Kevin Yuk-Lap Yip

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / WIndows/ MacOsX
  • Perl
  • R Package

:: DOWNLOAD

 ProbRNA

:: MORE INFORMATION

Citation

Bioinformatics. 2014 Jan 21.
Computational identification of protein binding sites on RNAs using high-throughput RNA structure-probing data.
Hu X1, Wong TK, Lu ZJ, Chan TF, Lau TC, Yiu SM, Yip KY.

rnapagenumber – Compute Optimal “page number” of an RNA Structure

rnapagenumber

:: DESCRIPTION

rnapagenumber is a web server that computes the optimal “page number” of an RNA structure, input as a PDB file or .ct (mfold connect) file.

::DEVELOPER

Clote Lab 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

On the page number of RNA secondary structures with pseudoknots.
P. Clote, S. Dobrev, I. Dotu, E. Kranakis. D. Krizanc, J. Urrutia,
J Math Biol. 2012 Dec;65(6-7):1337-57.

RNA-WL 1.5 – Thermodynamics of RNA structures by Wang-Landau sampling

RNA-WL 1.5

:: DESCRIPTION

RNA-WL is an implementation of the Wang-Landau non-Boltzmannian sampling algorithm to approximate the partition function for RNA secondary structures.

::DEVELOPER

Clote Lab 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux /  Mac OsX / Windows
  • WebServer
  • C Compiler

:: DOWNLOAD

 RNA-WL

:: MORE INFORMATION

Citation:

Feng Lou, Peter Clote.
Thermodynamics of RNA structures by Wang-Landau sampling.
ISMB 2010, Bioinformatics 2010 Jun 15;26(12):i278-86