Tag: Secondary Structure

mRNA optimiser 1.0 – Redesign mRNA Sequences to Optimise the Secondary Structure

mRNA optimiser 1.0

:: DESCRIPTION

The mRNA optimiser is a tool that redesigns a gene messenger RNA to optimise its secondary structure, without affecting the polypeptide sequence. The tool can either maximize or minimize the molecule minimum free energy (MFE), thus resulting in decreased or increased secondary structure strength.

::DEVELOPER

UA.PT Bioinformatics

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Linux/ Windows/MacOsX
  • Java

:: DOWNLOAD

 mRNA optimiser

:: MORE INFORMATION

Citation

P. Gaspar, G. Moura, M. A. S. Santos, and J. L. Oliveira
mRNA secondary structure optimization using a correlated stem–loop prediction
Nucleic Acids Research, Jan 2013, doi: 10.1093/nar/gks1473

RNAfamily – Java Viewer for RNA Secondary Structures

RNAfamily

:: DESCRIPTION

RNAfamily is a simple software tools that enables to display all secondary structures of a family of RNA molecules. It uses the linear backbone representation. RNAfamily provides usual graphical features: zooming, scrolling, etc. Colors of the stems correspond to matching stems. It is also possible to display the nucleotides composing a stem or the whole sequence.

::DEVELOPER

Bonsai Bioinformatics – INRIA

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / MacOsX / Linux
  • Java

:: DOWNLOAD

RNAfamily

:: MORE INFORMATION

For questions about RNAfamily or for bug reports, please contact Helene Touzet

Carnac 0.98 – Predict Secondary Structure for a set of Homologous RNA Sequences

Carnac 0.98

:: DESCRIPTION

Carnac is a software tool for analysing the hypothetical secondary structure of a family of homologous RNA. It aims at predicting if the sequences actually share a common secondary structure. When this structure exists, Carnac is then able to correctly recover a large amount of the folded stems. The input is a set of single-stranded RNA sequences that need not to be aligned. The folding strategy relies on a thermodynamic model with energy minimization. It combines information coming from locally conserved elements of the primary structure and mutual information between sequences with covariations too.

::DEVELOPER

Bonsai Bioinformatics – INRIA

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows /  Linux / MacOsX
  • C Complier

:: DOWNLOAD

Carnac

:: MORE INFORMATION

Citation

CARNAC: folding families of related RNAs
Touzet H. and Perriquet O.
Nucl. Acids Res. (2004) 32 (suppl 2): W142-W145

Prof 1.0 – Secondary Structure Prediction System

Prof 1.0

:: DESCRIPTION

Prof is a software for protein secondary structure prediction .

::DEVELOPER

Mohammed OUALI & Prof Ross King

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C COmpiler

:: DOWNLOAD

 Prof

:: MORE INFORMATION

Citation

Protein Sci. 2000 Jun;9(6):1162-76.
Cascaded multiple classifiers for secondary structure prediction.
Ouali M, King RD.

rPredictor – Prediction of Ribosomal RNA Secondary Structure

rPredictor

:: DESCRIPTION

rPredictor is a bioinformatic infrastructure for prediction, analysis and storage of secondary structures of ribosomal RNAs.

::DEVELOPER

SIRET Research Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

Josef Pánek, Jan Hajič jr., David Hoksza (2014)
Template-Based Prediction of Ribosomal RNA Secondary Structure,
IEEE International Conference on Bioinformatics and Biomedicine (BIBM), Belfast, UK, pp.: 18-20, IEEE

assp 1.2 – Assess Protein Secondary Structure Prediction Accuracy

assp 1.2

:: DESCRIPTION

assp (Assess  Secondary Structure Prediction) takes a multiple protein sequence alignmentand estimates the range in accuracy that one can expect for a “perfect” secondary structure prediction made using the alignment.

::DEVELOPER

The Barton Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

assp

:: MORE INFORMATION

Citation:

Russell, R. B. and Barton, G. J. (1993),
J. Mol. Biol., 234, 951-957,
“The Limits of Protein Structure Prediction Accuracy From Multiple Sequence Alignment”

JPred 4 – Protein Secondary Structure Prediction Server

JPred 4

:: DESCRIPTION

JPred is a Protein Secondary Structure Prediction server. JPred incorporates the Jnet algorithm in order to make more accurate predictions. In addition to protein secondary structure JPred also makes predictions on Solvent Accessibility and Coiled-coil regions (Lupas method).

:: DEVELOPER

The Barton Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

Nucleic Acids Res. 2015 Apr 16. pii: gkv332.
JPred4: a protein secondary structure prediction server.
Drozdetskiy A, Cole C, Procter J, Barton GJ.

SSCon – Consensus-based Secondary Structure predictor

SSCon

:: DESCRIPTION

SScon is a first-of-its-kind comprehensive design of a SS consensus predictor which considers 12 modern standalone SS predictors and utilize Support Vector Machine (SVM) to combine their predictions.

::DEVELOPER

Kurgan Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux/ MacOsX
  • Java

:: DOWNLOAD

  SSCon

 :: MORE INFORMATION

Citation

J Biomol Struct Dyn. 2014;32(1):36-51. doi: 10.1080/07391102.2012.746945. Epub 2013 Jan 9.
Comprehensively designed consensus of standalone secondary structure predictors improves Q3 by over 3%.
Yan J1, Marcus M, Kurgan L.

CRNPRED 1.1 – Predict Secondary Structures of Protein

CRNPRED 1.1

:: DESCRIPTION

CRNPRED is a program that predicts secondary structures (SS), contact numbers (CN), and residue-wise contact orders (RWCO) of a native protein structure from its amino acid sequence.

CRNPRED Online Version

::DEVELOPER

CRNPRED team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 CRNPRED

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2006 Sep 5;7:401.
CRNPRED: highly accurate prediction of one-dimensional protein structures by large-scale critical random networks.
Kinjo AR, Nishikawa K.

RNAalishapes 2.4.7 – Secondary Structure Prediction using Shape Abstraction

RNAalishapes 2.4.7

:: DESCRIPTION

RNAalishapes is a tool for secondary structure prediction, using shape abstraction. Input is a multiple sequence alignment. Pseudoknots are not considered at all.

::DEVELOPER

Stefan Janssen

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 RNAalishapes

:: MORE INFORMATION

Citation

The RNA shapes studio.
Janssen S, Giegerich R.
Bioinformatics. 2014 Oct 1. pii: btu649