Tag: Secondary Structures

McGenus / TT2NE – Prediction of RNAs Secondary Structures with Pseudoknots

McGenus / TT2NE

:: DESCRIPTION

The McGenus and TT2NE algorithms output predictions of RNA secondary structures with pseudoknots, based on penalizing or restricting the topological genus of the pairing graphs. The topological genus is an indicator of the complexity of the topology of the pairing

::DEVELOPER

The Institut de Physique Théorique (IPhT)

:: SCREENSHOTS

 N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

NO

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2013 Feb 1;41(3):1895-900. doi: 10.1093/nar/gks1204. Epub 2012 Dec 16.
McGenus: a Monte Carlo algorithm to predict RNA secondary structures with pseudoknots.
Bon M1, Micheletti C, Orland H.

TT2NE: a novel algorithm to predict RNA secondary structures with pseudoknots.
Bon M, Orland H.
Nucleic Acids Res. 2011 Aug;39(14):e93. doi: 10.1093/nar/gkr240.

pKiss 2.2.12 – Folding RNA Secondary Structures

pKiss 2.2.12

:: DESCRIPTION

pKiss is a tool for folding RNA secondary structures, including two limited classes of pseudoknots.

::DEVELOPER

Stefan Janssen

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 pKiss

:: MORE INFORMATION

Citation

J Comput Biol. 2008 Mar;15(2):139-63. doi: 10.1089/cmb.2007.0198.
Novel and efficient RNA secondary structure prediction using hierarchical folding.
Jabbari H, Condon A, Zhao S.

ILM 1.0 – Predict RNA Secondary Structures with Pseudoknots

ILM 1.0

:: DESCRIPTION

 ILM (Iterated Loop Matching) is a web server for predicting RNA secondary structures with pseudoknots.

::DEVELOPER

Jianhua Ruan

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/MacOsX
  • C Compiler

:: DOWNLOAD

 ILM

:: MORE INFORMATION

Citation

Ruan J, Stormo GD and Zhang W.
“An Iterated loop matching approach to the prediction of RNA secondary structures with pseudoknots“,
Bioinformatics. 2004 Jan 1;20(1):58-66.

RNAgraphdist 1.0 – Calculation of Graph-distance Distribution of the Boltzmann ensemble of RNA Secondary Structures

RNAgraphdist 1.0

:: DESCRIPTION

The RNAgraphdist calculates the equilibrium distribution of graph-distances between arbitrary pair of nucleotides in an RNA molecule. The program reads RNA structures generated from RNAsubopt, calculates their equilibrium distribution and outputs the graph-distances in a tab delimited list or in the terminal.

::DEVELOPER

Jing Qin

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 RNAgraphdist

:: MORE INFORMATION

Citation

Algorithms Mol Biol. 2014 Sep 11;9:19. doi: 10.1186/1748-7188-9-19. eCollection 2014.
Graph-distance distribution of the Boltzmann ensemble of RNA secondary structures.
Qin J, Fricke M, Marz M, Stadler PF, Backofen R.

YAP – Pairwise Sequence Alignment Using Secondary Structures

YAP

:: DESCRIPTION

YAP (Yet Another Alignment Program) have the possibility of aligning two sequences of amino acids taking into account different properties, namely secondary structures, transmembranicity etc.

::DEVELOPER

Piero Fariselli

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C Compiler

:: DOWNLOAD

 YAP

:: MORE INFORMATION