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.

PALSSE 20090521 – Predictive Assignment of Linear Secondary Structure Elements

PALSSE 20090521

:: DESCRIPTION

PALSSE (Predictive Assignment of Linear Secondary Structure Elements) is a software that delineates secondary structure elements (SSEs) from protein Cα coordinates and specifically addresses the requirements of vector-based protein similarity searches. Our program identifies two types of secondary structures: helix and β-strand, typically those that can be well approximated by vectors. In contrast to traditional secondary structure algorithms, which identify a secondary structure state for every residue in a protein chain, our program attributes residues to linear SSEs. Consecutive elements may overlap, thus allowing residues located at the overlapping region to have more than one secondary structure type.

::DEVELOPER

Grishin Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • python

:: DOWNLOAD

 PALSSE

:: MORE INFORMATION

Citation:

PALSSE: A program to delineate linear secondary structural elements from protein structures
Indranee Majumdar, S Sri Krishna and Nick V Grishin
BMC Bioinformatics 2005, 6:202

MASS 1.0 – Multiple Protein Structure Alignment by Secondary Structures

MASS 1.0

:: DESCRIPTION

MASS is an efficient method for multiple alignment of protein structures and detection of structural motifs. Exploiting the secondary structure representation aids in filtering out noisy results and in making the method highly efficient and robust. MASS disregards the sequence order of the secondary structure elements. Thus, it can find non-sequential and even non-topological structural motifs. An important novel feature of MASS is subset alignment detection: It does not require that all the input molecules be aligned. Rather, MASS is capable of detecting structural motifs shared only by a subset of the molecules.

::DEVELOPER

 the BioInfo3D group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 MASS

:: MORE INFORMATION

Citation:

O. Dror, H. Benyamini, R. Nussinov, and H. Wolfson .
MASS: Multiple structural alignment by secondary structures.
Bioinformatics, 19 Suppl. 1: i95 i104, 2003.

 

RNACluster 1.0 – RNA Secondary Structure Comparison and Clustering

RNACluster 1.0

:: DESCRIPTION

RNACluster is an integrated computational software which implements 6 common structure distances to measure the (dis)similarity of RNA secondary structures including base pair distance, mountain distance, morphological distance, tree edit distance, string edit distance and our in-house structure matrix distance, and one effective cluster approach for the ensemble clustering using a minimum spanning tree (MST) based algorithm. RNACluster can be used to study the characteristics of RNA secondary structures, RNA structure conformational switches, RNA conformational energy landscapes and RNA secondary structure prediction based on the clustering of structure ensemble.

::DEVELOPER

Qi Liu

:: REQUIREMENTS

  • Linux/Windows

:: DOWNLOAD

 RNACluster

:: MORE INFORMATION

Citation

Liu Q, Olman V, Liu H, Ye X, Qiu S, Xu Y.
RNACluster: An integrated tool for RNA secondary structure comparison and clustering.
J Comput Chem. 2008 Jul 15;29(9):1517-26.

MUPRED – Protein Secondary Structure Prediction

MUPRED

:: DESCRIPTION

MUPRED is a protein secondary structure and solvent accessibility prediction server based on a novel framework

MUPRED Online version

:DEVELOPER

Digital Biology Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Web Server

:: DOWNLOAD

 MUPRED

:: MORE INFORMATION

Citation

Bondugula R, Xu D.
MUPRED: a tool for bridging the gap between template based methods and sequence profile based methods for protein secondary structure prediction.
Proteins. 2007 Feb 15;66(3):664-70.

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

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.

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).

RNA-DV 1.0 – Design & Visualization Tool for RNA Secondary Structure

RNA-DV 1.0

:: DESCRIPTION

RNA-DV (RNA Design & Visualization) is a flexible and powerful tool targeted at visualization and modification of RNA secondary structure. Compare to existing software applications, RNA-DV set itself apart by not only providing an editing and visualization interface but also integrates thermodynamic energies for the current structure design. RNA-DV aims at providing an easy-to-use GUI for visualizing and designing RNA secondary structures. It allows users to interact directly with the RNA structure and perform operations such as changing primary sequence content and connect/disconnect nucleotide bonds. It also integrates thermodynamic energy calculations including four major energy models. RNA-DV recognizes three input formats including CT, RNAML and dot bracket (dp).

::DEVELOPER

Herbert H. Tsang and Denny C. Dai .

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / MacOsX / Linux
  • Java

:: DOWNLOAD

RNA-DV

:: MORE INFORMATION