MetaSSPred – Balanced Secondary Structure Predictor

MetaSSPred

:: DESCRIPTION

MetaSSPred is a well-balanced Secondary Structure predictor

::DEVELOPER

Hoque’s Lab, University of New Orleans

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 MetaSSPred

:: MORE INFORMATION

Citation

J Theor Biol. 2015 Nov 5;389:60-71. doi: 10.1016/j.jtbi.2015.10.015. [Epub ahead of print]
A balanced secondary structure predictor.
Nasrul Islam M, Iqbal S, Katebi AR, Tamjidul Hoque M

MapFold – Predicting Secondary Structure of RNA using Chemical and Enzymatic Mapping data

MapFold

:: DESCRIPTION

MapFold is a tool for predicting secondary structure of RNA using chemical and enzymatic mapping data. It is designed to take as input a combination of sequence and chemical probing data, and as output returns structures from the ensemble that are the closest match to the structural details contained within the probing data.

::DEVELOPER

The Laederach Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

RNA. 2010 Jun;16(6):1108-17. doi: 10.1261/rna.1988510. Epub 2010 Apr 22.
Evaluation of the information content of RNA structure mapping data for secondary structure prediction.
Quarrier S, Martin JS, Davis-Neulander L, Beauregard A, Laederach A.

RNAView – Generates 2-dimensional Displays of RNA/DNA Secondary Structures

RNAView

:: DESCRIPTION

RNAView program generates 2-dimensional displays of RNA/DNA secondary structures with tertiary interactions.  RNAView automatically identifies and classifies the types of base pairs that are formed in nucleic acid structures, fully implementing Leontis and Westhof’s ( RNA (2001) 7, 499-512), convention for edge-to-edge hydrogen bonding interactions.

::DEVELOPER

The Nucleic Acid Database Project , Rutgers, The State University of New Jersey

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Mac

:: DOWNLOAD

RNAView

:: MORE INFORMATION

Citation

Yang, H., Jossinet, F., Leontis, N., Chen, L., Westbrook, J., Berman, H.M., Westhof, E. (2003).
Tools for the automatic identification and classification of RNA base pairs.
Nucleic Acids Research 31.13: 3450-3460.

RNAprofile 2.2 – Secondary structure motif discovery in RNA sequences

RNAprofile 2.2

:: DESCRIPTION

RNAprofile is a software for the discovery of conserved sequence/structural motifs in unaligned RNA sequences

::DEVELOPER

the Pesolelab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows

:: DOWNLOAD

 RNAprofile

:: MORE INFORMATION

Citation:

Giulio Pavesi, Giancarlo Mauri, Marco Stefani and Graziano Pesole
RNAProfile: an algorithm for finding conserved secondary structure motifs in unaligned RNA sequences
Nucl. Acids Res. (2004) 32 (10): 3258-3269.

RNAclust 1.3 – Cluster RNAs based on Secondary Structures

RNAclust 1.3

:: DESCRIPTION

RNAclust is a perl script summarizing all the single steps required for clustering of structured RNA motifs, i.e. identifying groups of RNA sequences sharing a secondary structure motif. It requires as input a multiple FASTA file. In the first step for each input sequence the base pair probability matrix of its secondary structure distribution is calculated (using RNAfold from the Vienna RNA package). Secondly, for each pair of base pair probability matrices a sequence-structure alignment is calculated using LocARNA. Lastly, a hierarchical cluster-tree (in NEWICK format) is derived by WPGMA clustering of the pairwise alignment distances and the optimal number of clusters is calculated from the tree.

::DEVELOPER

Kristin Reiche

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 RNAclust

:: MORE INFORMATION

SSP – Secondary Structure Propensity

SSP

:: DESCRIPTION

The SSP is an algorithm that combines chemical shifts from different nuclei into a score, which reflects the expected fraction of α- or β-structure.

::DEVELOPER

Julie Forman-Kay’s Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 SSP

:: MORE INFORMATION

Citation

Protein Sci. 2006 Dec;15(12):2795-804. Epub 2006 Nov 6.
Sensitivity of secondary structure propensities to sequence differences between alpha- and gamma-synuclein: implications for fibrillation.
Marsh JA, Singh VK, Jia Z, Forman-Kay JD.

RNA draw 1.1b2 – RNA Secondary Structure Calculation & Analysis

RNA draw 1.1b2

:: DESCRIPTION

RNAdraw is an integrated program for RNA secondary structure calculation and analysis under 32-bit Microsoft Windows.

::DEVELOPER

Ole Matzura, mailto:ole@eviware.com

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

RNA draw

:: MORE INFORMATION

Citation

RNAdraw: an integrated program for RNA secondary structure calculation and analysis under 32-bit Microsoft Windows“,
Ole Matzura and Anders Wennborg,
Computer Applications in the Biosciences (CABIOS), Vol. 12 no. 3 1996, 247-249

loopDloop 2.07b – Draw RNA Secondary Structures

loopDloop 2.07b

:: DESCRIPTION

loopDloop is a tool for drawing RNA secondary structures in molecular biology. It will read files that include biosequence data with base pairing information.  It will display graphical views of the sequences secondary molecular structure.  Various options allow one to modify,adorn and edit the structure.   Standard application functions to save,print, edit and manage preferences are included.  This program will not estimate nor produce the base pairings needed for secondary structure. For that, other software such as RNAFOLD, MulFOLD, and multiple sequencealignment editors may be used.

::DEVELOPER

Don Gilbert at Indiana University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / Mac OsX
  • Java

:: DOWNLOAD

loopDloop

:: MORE INFORMATION

Citaiton

Gilbert, D.G., 1996. loopDloop in Java, a Java application for visualizing RNA secondary structure. ftp://iubio.bio.indiana.edu/molbio/loopdloop/java/.

SStructView 1.2.2 – RNA Secondary Structure Viewing Java Applet

SStructView 1.2.2

:: DESCRIPTION

SStructView is a Java applet for viewing RNA secondary structures and linking to multiple computational backends. SStructView supports colored bases, standard mouse selection mechanisms (drag to select a range, control-click to select individuals), arbitrary set-based data types to allow you to create your own groups, and other improvements.RNA biologists who want an extendible java application for viewing RNA secondary structure.

::DEVELOPER

Ramon M. Felciano, Richard Chen and Russ Altman, Helix Group

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / MacOsX / Linux
  • Java

:: DOWNLOAD

SStructView

:: MORE INFORMATION

Citation

R. M. Felciano, R. O. Chen, & R. B. Altman.
RNA Secondary Structure as a Reusable Interface to Biological Information Resources.
Gene 190 (1997) GC59-70

RNAwolf 0.3.2 / MC-Fold-DP – RNA Secondary Structure Prediction.

 RNAwolf 0.3.2 / MC-Fold-DP

:: DESCRIPTION

 RNAwolf and MC-Fold-DP are two programs (rather, collections of a library and several programs, each) that deal with RNA secondary structure prediction.

::DEVELOPER

Ivo Hofacker

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 RNAwolf 0.3.2 / MC-Fold-DP

:: MORE INFORMATION

Citation

Höner zu Siederdissen, Christian, Stephan H. Bernhart, Peter F. Stadler, and Ivo L. Hofacker. 2011.
A Folding Algorithm for Extended RNA Secondary Structures. 
Bioinformatics 27: 129–36.

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