Tag: Folding

rnaifold 3.1 – RNA Inverse Folding and Molecular Design

rnaifold 3.1

:: DESCRIPTION

rnaifold is a web server that solves the RNA inverse folding problem, using constraint programming. Given a target RNA secondary structure, as well as optional nucleotide constraints, RNAiFold determines all (or a large number of) RNA sequences, whose minimum free energy structure is the target structure.

::DEVELOPER

Clote Lab 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 rnaifold

:: MORE INFORMATION

Citation

RNAiFold 2.0: a web server and software to design custom and Rfam-based RNA molecules.
Garcia-Martin JA, Dotu I, Clote P.
Nucleic Acids Res. 2015 May 27. pii: gkv460.

RNAiFold: A constraint programming algorithm for RNA inverse folding and molecular design
J.A. Garcia-Martin, P. Clote, I. Dotu,
Journal of Bioinformatics and Computational Biology ,DOI: 10.1142/S0219720013500017

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.

RNAscf 1.1 – Consensus Folding of Unaligned RNA sequences

RNAscf 1.1

:: DESCRIPTION

RNAscf is a program for RNA consensus folding for a set of unaligned RNA sequences.

::DEVELOPER

UCF Computational Biology and Bioinformatics Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C Compiler

:: DOWNLOAD

 RNAscf

:: MORE INFORMATION

Citation

J Comput Biol. 2006 Mar;13(2):283-95.
Consensus folding of unaligned RNA sequences revisited.
Bafna V, Tang H, Zhang S.

DAFS 0.0.3 – Simultaneous Aligning and Folding of RNA Sequences by Dual Decomposition

DAFS 0.0.3

:: DESCRIPTION

DAFS is a novel algorithm that simultaneously aligns and folds RNA sequences based on maximizing expected accuracy of a predicted common secondary structure and its alignment.

::DEVELOPER

Computational Biology Research Center (CBRC),

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 DAFS

:: MORE INFORMATION

Citation:

DAFS: simultaneous aligning and folding of RNA sequences via dual decomposition.
Sato K, Kato Y, Akutsu T, Asai K, Sakakibara Y.
Bioinformatics. 2012 Dec 15;28(24):3218-24. doi: 10.1093/bioinformatics/bts612.

PETfold 2.0 / PETcofold 3.2 – Folding of Multiple Alignment of RNA sequences

PETfold 2.0 / PETcofold 3.2

:: DESCRIPTION

PETfold: Phylogenetic, Evolutionary and Thermodynamic folding of a multiple alignment of RNA sequences.

PETcofold: Integrated framework with PETfold to fold and search for RNA-RNA interactions between two multiple alignments of RNA sequences.

::DEVELOPER

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

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 PETfold , PETcofold

:: MORE INFORMATION

Citation:

Seemann SE, Menzel P, Backofen R, Gorodkin J
“The PETfold and PETcofold web servers for intra- and intermolecular structures of multiple RNA sequences.”,
Nucleic Acid Res., 39(Web Server issue):W107-11, 2011.

MSMExplorer 0.9 – Visualization Application for Markov State Models for Folding

MSMExplorer 0.9

:: DESCRIPTION

MSMExplorer Provide a simple, powerful tool for maximizing the utility of Markov State Models for understanding folding phenomena.

::DEVELOPER

MSMExplorer Team

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / MacOsX /  Linux
  • Java

:: DOWNLOAD

 MSMExplorer 

:: MORE INFORMATION

Citation

Bioinformatics (2013) 29 (7): 950-952.
MSMExplorer: visualizing Markov state models for biomolecule folding simulations.
Cronkite-Ratcliff B, Pande V.

Randfold 2.0 – RNA Minimum Free Energy of Folding Randomization Test

Randfold 2.0

:: DESCRIPTION

Randfold compute the probability that, for a given RNA sequence, the Minimum Free Energy (MFE) of the secondary structure is different from a distribution of MFE computed with random sequences.

:: DEVELOPER

Bioinformatics & Systems Biology

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 Randfold

:: MORE INFORMATION

Citation:

Bonnet, E., * Wuyts, J., Rouzé, P., Van de Peer, Y. (2004)
Evidence that microRNA precursors, unlike other non-coding RNAs, have lower folding free energies than random sequences.
Bioinformatics 20, 2911-7

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