Tag: Pseudoknot

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.

IPknot 1.4.1 – RNA Secondary Structure Prediction including Pseudoknots

IPknot 1.4.1

:: DESCRIPTION

IPknot provides services for predicting RNA secondary structures including a wide class of pseudoknots. IPknot can also predict the consensus secondary structure when a multiple alignment of RNA sequences is given. IPknot runs fast and predicts the maximum expected accuracy (MEA) structure using integer programming (IP) with threshold cut.

::DEVELOPER

Yuki Kato, Kengo Sato.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOsX

:: DOWNLOAD

 IPknot

:: MORE INFORMATION

Citation

Y. Kato, K. Sato, K. Asai and T. Akutsu,
Rtips: fast and accurate tools for RNA 2D structure prediction using integer programming,
Nucleic Acids Res., 40, W29-W34, 2012

K. Sato, Y. Kato, M. Hamada, T. Akutsu and K. Asai,
IPknot: fast and accurate prediction of RNA secondary structures with pseudoknots using integer programming,
Bioinformatics, vol. 27, no. 13, pp. i85-i93, 2011

PseudoViewer 3.0 – Visualization of RNA Pseudoknots of any type

PseudoViewer 3.0

:: DESCRIPTION

PseudoViewer is a program for visualizing RNA secondary structures with pseudoknots. Experimental results show that the PseudoViewer web service and web application are useful for resolving many problems with incompatible software components as well as for visualizing large-scale RNA secondary structures with pseudoknots of any type.

PseudoViewer Online Version

::DEVELOPER

Biocomputing Lab. School of Computer Science and Engineering Inha University, Inchon

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

PseudoViewer

:: MORE INFORMATION

Citation

Y. Byun and K. Han,
PseudoViewer3: generating planar drawings of large-scale RNA structures with pseudoknots,
Bioinformatics, Vol. 25, 1435-1437, 2009.

PhyloQFold – Bayesian Sampling of Evolutionarily Conserved RNA Secondary Structures with Pseudoknot

PhyloQFold

:: DESCRIPTION

PhyloQFold is a program for Bayesian sampling of evolutionarily conserved RNA secondary structures with pseudoknots.

::DEVELOPER

Dirk Metzler

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/MacOsX
  • C++ Compiler

:: DOWNLOAD

 PhyloQFold

:: MORE INFORMATION

Citation

Bioinformatics. 2012 Sep 1;28(17):2242-8. doi: 10.1093/bioinformatics/bts369.
Bayesian sampling of evolutionarily conserved RNA secondary structures with pseudoknots.
Doose G, Metzler D.

PAL 1.31 – Pseudoknot Aligment for RNA Sequences

PAL 1.31

:: DESCRIPTION

PAL is an implementation of an efficient algorithm to compute an optimal structural alignment of an RNA sequence against a genomic substring.

::DEVELOPER

UCF Computational Biology and Bioinformatics Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C Compiler

:: DOWNLOAD

 PAL

:: MORE INFORMATION

Citation

J Comput Biol. 2008 Jun;15(5):489-504. doi: 10.1089/cmb.2007.0214.
Structural alignment of pseudoknotted RNA.
Han B, Dost B, Bafna V, 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

PKNOTS 1.07 – RNA Pseudoknot Prediction

PKNOTS 1.07

:: DESCRIPTION

PKNOTS is an experimental code demonstrating a dynamic programming algorithm for RNA pseudoknot prediction.

::DEVELOPER

Elena Rivas, Eddy lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C Compiler

:: DOWNLOAD

  PKNOTS

:: MORE INFORMATION

Citation

J Mol Biol. 1999 Feb 5;285(5):2053-68.
A dynamic programming algorithm for RNA structure prediction including pseudoknots.
Rivas E, Eddy SR.

RNATOPS 1.2 – RNA Pseudoknot Search in Genomes

RNATOPS 1.2

:: DESCRIPTION

RNATOPS (RNA via Tree decOmPoSition) is a program that searches for RNA secondary structures based on the notion of a structure graph to specify the consensus structure of an RNA family.The model for profiling the consensus structure of an RNA family is a conformational graph that specifies the topology of the consensus fold and relationship among helices and unpaired loops. Individual helices and loops are modeled with a restricted Covariance Model and profile HMM, respectively. The fold topology, helices, and loops are trained with an input pasta file that contains a multiple structural alignment for a set of training RNA sequences.

::DEVELOPER

The RNA-Informatics Research Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / MacOsX / Linux
  • C++ Complier

:: DOWNLOAD

 RNATOPS

:: MORE INFORMATION

Citation

Huang, Z., Wu, Y., Robertson, J., Feng, L., Malmberg, R., and Cai, L. (2008)
Fast and accurate search for non-coding RNA pseudoknot structures in genomes,
Bioinforamtics, 24(20):2281-2287.

HotKnots 2.0 – Predict Secondary Structures of RNA with or without Pseudoknots

HotKnots 2.0

:: DESCRIPTION

The HotKnots program predicts secondary structures of RNA molecules with or without pseudoknots.

HotKnots Online Version

::DEVELOPER

BETA LAB – University of British Columbia

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 HotKnots

:: MORE INFORMATION

Citation:

Ren, J., Rastegari, B., Condon, A., and Hoos, H. H. (2005).
HotKnots: heuristic prediction of RNA secondary structures including pseudoknots.
RNA, 11(10), 1494–1504.

Knotted2Nested – Remove Pseudoknots from RNA

Knotted2Nested

:: DESCRIPTION

Knotted2Nested removes pseudoknots from a list of RNA base pairs, using different algorithms. It produces in pseudoknot-free (dot-bracket) 2D structures.

::DEVELOPER

The Centre for Integrative Bioinformatics VU

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • Python

:: DOWNLOAD

Knotted2Nested

:: 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.