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

MARIO 0.4 – Mapping RNA-RNA interactome and RNA Structure

MARIO 0.4

:: DESCRIPTION

MARIO (Mapping RNA-RNA interactome in vivo) is a tools to study RNA-RNA interactome and structures in vivo.

::DEVELOPER

Zhong Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python
  • BioPython

:: DOWNLOAD

MARIO

:: MORE INFORMATION

Citation

Nat Commun. 2016 Jun 24;7:12023. doi: 10.1038/ncomms12023.
Mapping RNA-RNA interactome and RNA structure in vivo by MARIO.
Nguyen TC, Cao X, Yu P, Xiao S, Lu J, Biase FH, Sridhar B, Huang N, Zhang K, Zhong S.

MIfold 2 – Predicting RNA Structure using Mutual Information

MIfold 2

:: DESCRIPTION

MIfold is a matlab toolbox that uses mutual information and related measures to infer and display secondary structures (including pseudoknots). Given a sequence alignment MIfold computes and displays the mutual and sequence information of the alignment. MIfold also uses a dynamic programming algorithm to predict the secondary structure with maximal total mutual information.

::DEVELOPER

the RNA Computational Biology group at the University of East Anglia (UEA)

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows/ Linux /MacOsX
  • matlab

:: DOWNLOAD

 MIfold

:: MORE INFORMATION

Citation

Freyhult, Eva, Moulton, Vincent and Gardner, Paul, 2005
Predicting RNA structure using mutual information,
Applied Bioinformatics. 4(1):53-9.

MutualFold – Simultaneous Folding of Alternative RNA Structures with Mutual Constraints

MutualFold

:: DESCRIPTION

MutualFold is an application to next-generation sequencing based RNA structure probing.

::DEVELOPER

UCF Computational Biology and Bioinformatics Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 MutualFold

:: MORE INFORMATION

Citation:

J Comput Biol. 2014 Aug;21(8):609-21. doi: 10.1089/cmb.2013.0044. Epub 2014 Apr 1.
Simultaneous folding of alternative RNA structures with mutual constraints: an application to next-generation sequencing-based RNA structure probing.
Zhong C1, Zhang S.

PMFastR – New Approach to Multiple RNA Structure Alignment

PMFastR

:: DESCRIPTION

PMFastR is an algorithm which iteratively uses a sequence-structure alignment procedure to build a multiple RNA structure alignment

::DEVELOPER

UCF Computational Biology and Bioinformatics Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C Compiler

:: DOWNLOAD

 PMFastR

:: MORE INFORMATION

Citation

IEEE/ACM Trans Comput Biol Bioinform. 2011 Apr 29. [Epub ahead of print]
A Memory Efficient Method for Structure-Based RNA Multiple Alignment.
Deblasio D, Bruand J, Zhang S.

PSTAG 2.1.4a – Model Pseudoknot RNA Structure

PSTAG 2.1.4a

:: DESCRIPTION

PSTAG (Pair Stochastic Tree Adjoining Grammars) for RNA sequences including pseudoknotted structures.

::DEVELOPER

Sakakibara Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/WIndows

:: DOWNLOAD

 PSTAG

:: MORE INFORMATION

Citation:

Matsui, H, Sato, K. and Sakakibara, Y.,
Pair Stochastic Tree Adjoining Grammars for Aligning and Predicting Pseudoknot RNA Structures,
Bioinformatics, vol.21, no.11, pp.2611-2617, 2005