MultiRNAFold 2.0 – Secondary Structure Prediction of RNA/DNA

MultiRNAFold 2.0

:: DESCRIPTION

The MultiRNAFold package contains software for secondary structure prediction of one, two, or many interacting RNA or DNA molecules. It is composed of three pieces of software: SimFold, PairFold and MultiFold.

::DEVELOPER

BETA LAB – University of British Columbia

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/Windows

:: DOWNLOAD

 MultiRNAFold

:: MORE INFORMATION

Citation:

Mirela Andronescu, Zhi Chuan Zhang and Anne Condon,
Secondary Structure Prediction of Interacting RNA Molecules“,
Journal of Molecular Biology, Vol 345/5 pp 987-1001.

OligoWalk 2 – Select Efficient siRNA using Hybridization Thermodynamics

OligoWalk 2

:: DESCRIPTION

OligoWalk is an online sever calculating thermodynamic features of sense-antisense hybidization. It predicts the free energy changes of oligonucleotides binding to a target RNA. It can be used to design efficient siRNA targeting a given mRNA sequence.

::DEVELOPER

Mathews group

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 OligoWalk

:: MORE INFORMATION

Citation:

Efficient siRNA selection using hybridization thermodynamics
Zhi John Lu and David H. Mathews
Nucl. Acids Res. (2008) 36 (2): 640-647

Kinefold – RNA/DNA Folding Predictions

Kinefold

:: DESCRIPTION

Kinefold is a software for stochastic folding simulations of nucleic acids on second to minute molecular time scales. Renaturation or co-transcriptional folding paths are simulated at the level of helix formation and dissociation in agreement with the seminal experimental results. Pseudoknots and topologically ‘entangled’ helices (i.e. knots) are efficiently predicted taking into account simple geometrical and topological constraints.

Kinefold Online Version

::DEVELOPER

The Isambert Lab

:: REQUIREMENTS

:: DOWNLOAD

 Kinefold

:: MORE INFORMATION

Citation:

A. Xayaphoummine, T. Bucher & H. Isambert,
Kinefold web server for RNA/DNA folding path and structure prediction including pseudoknots and knots,
Nucleic Acid Res., 33, 605-610 (2005)

K2N – Service to Get from Knotted to Nested RNA Structures

K2N

:: DESCRIPTION

K2N (Knotted To Nested) a service to get from knotted to nested RNA structures. This site provides access to a variety of methods for pseudoknot removal.

::DEVELOPER

The Centre for Integrative Bioinformatics VU

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 K2N

:: MORE INFORMATION

Citation

Sandra Smit, Kristian Rother, Jaap Heringa, and Rob Knight.
From knotted to nested RNA structures: a variety of computational methods for pseudoknot removal.
RNA (2008) 14(3):410-416.

SPuNC – RNA Structure Prediction using Nucleotide Composition

SPuNC

:: DESCRIPTION

SPuNC (Structure Prediction using Nucleotide Composition) provides a method for RNA structure prediction using evolutionary patterns of nucleotide composition.

::DEVELOPER

The Centre for Integrative Bioinformatics VU

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 SPuNC

:: MORE INFORMATION

Citation

Sandra Smit, Rob Knight, and Jaap Heringa
RNA structure prediction from evolutionary patterns of nucleotide composition.
NAR (2009) 37(5):1378-86

RNA – RNA Consensus Secondary Structure Prediction Software

RNA

:: DESCRIPTION

RNA is a program to predict the consensus secondary structure of a set of unaligned RNA sequences

::DEVELOPER

Henry Soldano

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 RNA

:: MORE INFORMATION

Citation

D. Bouthinon and H. Soldano,
A new method to predict the consensus secondary structure of a set of unaligned RNA sequences
BioInformatics, Vol 15 n°10, 1999, pages 785-798).

Migal 2.2 – Compare RNA Secondary Structure

Migal 2.2

:: DESCRIPTION

MiGaL (Multiple Graph Layer) is a software used to compare RNA secondary structure.

MiGaL Online Version

::DEVELOPER

Julien Allali

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 Migal

:: MORE INFORMATION

Citation

Julien Allali , Marie-France Sagot
A Multiple Graph Layers Model with Application to RNA Secondary Structures Comparison
Software—Practice & Experience Volume 38 Issue 8, July 2008

noRNAlize 1.0 – RNA SHAPE Data Normalization software

noRNAlize 1.0

:: DESCRIPTION

noRNAlize is a data analysis package to analyze and normalize SHAPE (Selective 2′-Hydroxyl Acylation and Primer Extension) data. Traditionally, SHAPE requires the addition of a 3′ hairpin to the RNA for normalization. noRNAlize elminates the need for this experimental step by performing a global analysis of the SHAPE data, and establishing mean protection values. This is particularly important when SHAPE analysis is used to map crystal contacts in crystal structures as illustrated here.

::DEVELOPER

noRNAlize Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / MacOsX /  Linux
  • MATLAB

:: DOWNLOAD

 noRNAlize

:: MORE INFORMATION

Citation:

Vicens Q, Gooding AR, Laederach A, Cech TR,
Local RNA structural changes induced by crystallization are revealed by SHAPE,
RNA, (2007)

RNAG – Block Gibbs Sampler for RNA Prediction

RNAG

:: DESCRIPTION

RNAG predicts consensus secondary structures for unaligned sequences. It uses a blocked Gibbs sampling algorithm, which has a theoretical advantage in convergence time. This algorithm iteratively samples from the conditional probability distributions P(Structure | Alignment) and P(Alignment | Structure).

RNAG Online Version

::DEVELOPER

Brown University Center for Computational Molecular Biology

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 RNAG

:: MORE INFORMATION

Citation

Donglai Wei, Lauren V. Alpert and Charles E. Lawrence
RNAG: a new Gibbs sampler for predicting RNA secondary structure for unaligned sequences
ioinformatics (2011) 27 (18): 2486-2493.

HALO 1.3 – Precise RNA de novo Transcript Half-life Determination

HALO 1.3

:: DESCRIPTION

HALO (Half-life Organizer) is the first software for the precise determination of transcript half-lives from measurements of RNA de novo transcription. In addition, methods for quality control, filtering and normalization are supplied. HALO provides a graphical user interface, command line tools and a well-documented Java API. Thus, it can be used both by biologists to determine transcript half-lives fast and reliably with the user interfaces provided as well as software developers integrating transcript half-life analysis into other gene expression profiling pipelines.

::DEVELOPER

Institut für Informatik, Ludwig-Maximilians-Universität München

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / Mac OsX
  • Java

:: DOWNLOAD

HALO

:: MORE INFORMATION

Citation

Caroline C. Friedel, Stefanie Kaufmann, Lars Dölken, Ralf Zimmer.
HALO – A Java framework for precise transcript half-life determination.
Bioinformatics, vol 26, no. 9, pp. 1264-1266, May 2010.