Erpin 5.5.4 – RNA Motif Search program

Erpin 5.5.4

:: DESCRIPTION

ERPIN (Easy RNA Profile IdentificatioN) takes as input an RNA sequence alignment and secondary structure annotation and will identify a wide variety of known RNA motifs (such as tRNAs, 5S rRNAs, SRP RNA, C/D box snoRNAs, hammerhead motifs, miRNAs and others) in your sequence(s) of interest. Also contains tool for drawing secondary structure of motifs.

::DEVELOPER

Daniel GAUTHERET and André Lambert

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 Erpin

:: MORE INFORMATION

Citation

Gautheret D, Lambert A. (2001)
Direct RNA Motif Definition and Identification from Multiple Sequence Alignments using Secondary Structure Profiles.
J Mol Biol. 313:1003-11

MEMERIS 1.0 – MEME in Rna’s Including Secondary Structures

MEMERIS 1.0

:: DESCRIPTION

MEMERIS (Muptiple Em for Motif Elucidation in Rna’s Including Secondary Structures) integrates information about RNA secondary structures into the motif search to guide the search towards single-stranded regions.

::DEVELOPER

Chair for Bioinformatics Freiburg

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 MEMERIS

:: MORE INFORMATION

Citation

Hiller M, Pudimat R, Busch A, and Backofen R.
Using RNA secondary structures to guide sequence motif finding towards single-stranded regions.
Nucleic Acids Res. 2006

LocalFold 1.0 – Local Folding of RNA

LocalFold 1.0

:: DESCRIPTION

LocalFold is a modification of the RNAplfold local folding algorithm. LocalFold only considers base-pairs centred within a window such that (i,j) are not located within the first and last positions of the windows.

::DEVELOPER

Chair for Bioinformatics Freiburg

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 LocalFold

:: MORE INFORMATION

Citation

Sita J. Lange, Daniel Maticzka, Mathias Möhl, Joshua N. Gagnon, Chris M. Brown and Rolf Backofen
Global or local? Predicting secondary structure and accessibility in mRNAs

RNAplex 0.2 – Search for Short Interactions between two long RNAs

RNAplex 0.2

:: DESCRIPTION

RNAplex is a tool especially created to rapidly search for short interactions between two long RNAs.

::DEVELOPER

Hakim Tafer

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/Windows/MacOsX
  • Perl

:: DOWNLOAD

 RNAplex

:: MORE INFORMATION

Citation

Bioinformatics. 2008 Nov 15;24(22):2657-63. Epub 2008 Apr 23.
RNAplex: a fast tool for RNA-RNA interaction search.
Tafer H, Hofacker IL.

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

ConStruct 3.2.5 – RNA Alignment Editor and Consensus Structure Prediction Tool

ConStruct 3.2.5

:: DESCRIPTION

ConStruct (construction of RNA consensus structures) is an RNA alignment editor and consensus structure prediction tool. It combines multiple sequence alignment, thermodynamic structure prediction and statistics in a semiautomatical fashion. Its sophisticated GUI guides the user through correcting an initial sequence alignment with respect to a consensus structure.

::DEVELOPER

Gerhard Steger <steger@biophys.uni-duesseldorf.de>,Heinrich-Heine-Universität Düsseldorf, Institut für Physikalische Biologie, Universitätsstr

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

  ConStruct

:: MORE INFORMATION

Citation:

Wilm, A., Linnenbrink, K. & Steger, G. (2008)
ConStruct: improved construction of RNA consensus structures.
BMC Bioinformatics 9, 219.

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.

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.

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)

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).