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

GTfold 3.0 – Scalable Multicore Code for RNA Secondary Structure Prediction

GTfold 3.0

:: DESCRIPTION

GTfold is a fast, scalable multicore code for predicting RNA secondary structure that is one to two orders of magnitude faster than the de facto standard programs and achieves comparable accuracy of prediction.

::DEVELOPER

Bader HPC Lab @ GeorgiaTech

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux/MacOsX/Windows with Cygwin

:: DOWNLOAD

GTfold

:: MORE INFORMATION

Citation

A. Mathuriya, D.A. Bader, C.E. Heitsch, and S.C. Harvey,
“GTfold: A Scalable Multicore Code for RNA Secondary Structure Prediction“,
24th Annual ACM Symposium on Applied Computing (SAC), Computational Sciences Track, Honolulu, HI, March 8-12, 2009.

HelixPSO – Particle Swarm Optimizer for RNA Secondary Structure Prediction

HelixPSO

:: DESCRIPTION

HelixPSO (Particle Swarm Optimizer) is a multi swarm algorithm that searches the conformation space of an RNA sequence for low lying structures. Fitness is a combination of free energy and agreement with the centroid structure in the thermodynamic ensemble. HelixPSO has been used on sequences of up to 1500 nucleotides.

::DEVELOPER

Bioinformatics Leipzig

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

HelixPSO

:: MORE INFORMATION

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.