RNAfamily – Java Viewer for RNA Secondary Structures

RNAfamily

:: DESCRIPTION

RNAfamily is a simple software tools that enables to display all secondary structures of a family of RNA molecules. It uses the linear backbone representation. RNAfamily provides usual graphical features: zooming, scrolling, etc. Colors of the stems correspond to matching stems. It is also possible to display the nucleotides composing a stem or the whole sequence.

::DEVELOPER

Bonsai Bioinformatics – INRIA

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / MacOsX / Linux
  • Java

:: DOWNLOAD

RNAfamily

:: MORE INFORMATION

For questions about RNAfamily or for bug reports, please contact Helene Touzet

Regliss – RNA Energy Landscape and Saturated Structures

Regliss

:: DESCRIPTION

Regliss proposes to study the energy landscape of a given RNA sequence by considering all locally optimal structures.

::DEVELOPER

Bonsai Bioinformatics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

J Comput Biol. 2012 Oct;19(10):1120-33. doi: 10.1089/cmb.2010.0178.
RNA locally optimal secondary structures.
Saffarian A, Giraud M, de Monte A, Touzet H.

SCFG Structural Entropy 20120907 – Calculate RNA Structural Entropies through Stochastic Context Free Grammars

SCFG Structural Entropy 20120907

:: DESCRIPTION

SCFG Structural Entropy is a software to calculate RNA structural entropies through stochastic context free grammars.

::DEVELOPER

Russell Malmberg Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 SCFG Structural Entropy

:: MORE INFORMATION

Citation

J Theor Biol. 2013 Feb 7;318:140-63. doi: 10.1016/j.jtbi.2012.10.023. Epub 2012 Nov 14.
Information-theoretic uncertainty of SCFG-modeled folding space of the non-coding RNA.
Manzourolajdad A1, Wang Y, Shaw TI, Malmberg RL.

RaligNAtor 1.2 – A kind of RNA-related BLAST

RaligNAtor 1.2

:: DESCRIPTION

RaligNAtor is an ultra fast alignment of RNA sequence structure patterns.

::DEVELOPER

RaligNAtor team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOsX

:: DOWNLOAD

 RaligNAtor 

:: MORE INFORMATION

Citation

Meyer, F., Kurtz, S., Beckstette, M. (2013).
Fast online and index-based algorithms for approximate search of RNA sequence-structure patterns.
BMC Bioinformatics 14:226.

eteRNA / NOVA RNA VirtuaLab – RNA Game Lets Players Help Find a Biological Prize

eteRNA / NOVA RNA VirtuaLab

:: DESCRIPTION

By playing EteRNA, you will participate in creating the first large-scale library of synthetic RNA designs. Your efforts will help reveal new principles for designing RNA-based switches and nanomachines — new systems for seeking and eventually controlling living cells and disease-causing viruses. By interacting with thousands of players and learning from real experimental feedback, you will be pioneering a completely new way to do science.

In NOVA RNA VirtuaLab you’ll play the role of a molecular engineer by solving RNA folding puzzles. Then take your skills to Eterna, where you can design RNAs that could be at the heart of future life-saving therapies.

::DEVELOPER

the Das Lab

:: SCREENSHOTS

:: REQUIREMENTS

  • Web Browser
  • Flash

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

JOHN MARKOFF
RNA Game Lets Players Help Find a Biological Prize
The New York Times January 11, 2011, on page D4

HelixMC – Python-based Monte Carlo simulator for DNA/RNA duplexes

HelixMC

:: DESCRIPTION

HelixMC is a software package for Monte-Carlo (MC) simulations of DNA/RNA helices using the base-pair level model. It provides a powerful tool to understand the flexibility of DNA/RNA helices through numerical simualtions.

::DEVELOPER

Das Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux /  MacOsX/ Windows
  • Python
  • Numpy
  • Matplotlib
  • C/C++ compiler

:: DOWNLOAD

 HelixMC

 :: MORE INFORMATION

Citation

PLoS Comput Biol. 2014 Aug 7;10(8):e1003756. doi: 10.1371/journal.pcbi.1003756. eCollection 2014.
Blind predictions of DNA and RNA tweezers experiments with force and torque.
Chou FC, Lipfert J, Das R

aPPRove – Accurate Prediction of RNA and Pentatricopeptide Repeat Protein Binding

aPPRove

:: DESCRIPTION

aPPRove is a computational tool that predicts the interaction of a PPR with its RNA binding site.

::DEVELOPER

SEQ Development Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

aPPRove

:: MORE INFORMATION

Citation

New Phytol. 2011 Jul;191(1):37-47. doi: 10.1111/j.1469-8137.2011.03746.x. Epub 2011 May 9.
The evolution of RNA editing and pentatricopeptide repeat genes.
Fujii S1, Small I.

ExomePeak 2.17.0 – Exome-based Analysis for RNA Epigenome Sequencing Data

ExomePeak 2.17.0

:: DESCRIPTION

ExomePeak is a software for affinity-based RNA epigenome sequencing data obtained from MeRIP-seq or m6A-seq

::DEVELOPER

ExomePeak team

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Linux/ Windows/MacOsX
  • R pacakge/MatLab
  • BioConductor

:: DOWNLOAD

 ExomePeak

:: MORE INFORMATION

Citation

Bioinformatics. 2013 Jun 15;29(12):1565-7. doi: 10.1093/bioinformatics/btt171. Epub 2013 Apr 14.
Exome-based analysis for RNA epigenome sequencing data.
Meng J1, Cui X, Rao MK, Chen Y, Huang Y.

rna-dm 0.9 – Minimum or Optimal Free Energy Landscape for a RNA sequence

rna-dm 0.9

:: DESCRIPTION

rna-dm (RNA Dynamic Miner) is a C++ program that can generate the profile of minimum or optimal free energy landscape for a given partial or complete RNA sequence. It also can process a data set of large RNA sequences in a high-throughput fashion.

::DEVELOPER

Liang Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ MacOsX/Windows
  • C++ Compiler

:: DOWNLOAD

 rna-dm

:: MORE INFORMATION