MIfold 2 – Predicting RNA Structure using Mutual Information

MIfold 2

:: DESCRIPTION

MIfold is a matlab toolbox that uses mutual information and related measures to infer and display secondary structures (including pseudoknots). Given a sequence alignment MIfold computes and displays the mutual and sequence information of the alignment. MIfold also uses a dynamic programming algorithm to predict the secondary structure with maximal total mutual information.

::DEVELOPER

the RNA Computational Biology group at the University of East Anglia (UEA)

:: SCREENSHOTS

MIfold

:: REQUIREMENTS

  • Windows/ Linux /MacOsX
  • matlab

:: DOWNLOAD

 MIfold

:: MORE INFORMATION

Citation

Freyhult, Eva, Moulton, Vincent and Gardner, Paul, 2005
Predicting RNA structure using mutual information,
Applied Bioinformatics. 4(1):53-9.

PhyloRNAalifold v1 – Predicting Consensus Structures in RNA Alignments by incorporating RNAalifold with Phylogenetic information

PhyloRNAalifold v1

:: DESCRIPTION

PhyloRNAalifold is a program for predicting consensus structures of aligned RNA sequences by incorporating phylogetetic-based covarying mutations.

::DEVELOPER

UCF Computational Biology and Bioinformatics Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ Compiler

:: DOWNLOAD

 PhyloRNAalifold

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2013 Apr 27;14:142. doi: 10.1186/1471-2105-14-142.
Incorporating phylogenetic-based covarying mutations into RNAalifold for RNA consensus structure prediction.
Ge P, Zhang S.

RNAConSLOpt 1.2 – Predicting Consensus stable local optimal Structures for Aligned RNA Sequences

RNAConSLOpt 1.2

:: DESCRIPTION

RNAConSLOpt is a program for predicting consensus stable local optimal structures (represented by stack configurations) for aligned RNA sequences. RNAConSLOpt can be used to predict consensus alternate structures for riboswitches.

::DEVELOPER

UCF Computational Biology and Bioinformatics Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C Compiler

:: DOWNLOAD

 RNAConSLOpt

:: MORE INFORMATION

Citation

Int J Bioinform Res Appl. 2014;10(4):498-518. doi: 10.1504/IJBRA.2014.062997.
Finding consensus stable local optimal structures for aligned RNA sequences and its application to discovering riboswitch elements.
Li Y, Zhong C, Zhang S.

RNASLOpt – Predicting stable local optimal Structures for RNAs

RNASLOpt

:: DESCRIPTION

RNASLOpt is a program for predicting stable local optimal secondary structures (represented by stack configurations) for RNAs. RNASLOpt can be used to predict alternate structures for riboswitches.

::DEVELOPER

UCF Computational Biology and Bioinformatics Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C Compiler

:: DOWNLOAD

 RNASLOpt

:: MORE INFORMATION

Citation

Bioinformatics. 2011 Nov 1;27(21):2994-3001. doi: 10.1093/bioinformatics/btr510. Epub 2011 Sep 8.
Finding stable local optimal RNA secondary structures.
Li Y, Zhang S.

RNAEAPath 1.0 – Predicting Folding Pathways between RNA Conformational Structures Guided by RNA Stacks

RNAEAPath 1.0

:: DESCRIPTION

RNAEAPath provides an alternate approach for predicting low-barrier folding pathways between RNA conformational secondary structures.

::DEVELOPER

UCF Computational Biology and Bioinformatics Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C Compiler

:: DOWNLOAD

 RNAEAPath

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2012 Mar 21;13 Suppl 3:S5. doi: 10.1186/1471-2105-13-S3-S5.
Predicting folding pathways between RNA conformational structures guided by RNA stacks.
Li Y, Zhang S.

ProMK – Predicting Protein Function using Multiple Kernels

ProMK

:: DESCRIPTION

ProMK is a method of Predicting Protein Function using Multiple Kernels

::DEVELOPER

Guoxian Yu

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux
  • MatLab

:: DOWNLOAD

 ProMK

:: MORE INFORMATION

Citation

IEEE/ACM Trans Comput Biol Bioinform. 2015 Jan-Feb;12(1):219-33. doi: 10.1109/TCBB.2014.2351821.
Predicting Protein Function Using Multiple Kernels.
Yu G, Rangwala H, Domeniconi C, Zhang G, Zhang Z.

InterMap3D – Predicting and Visualizing Co-evolving Protein Residues

InterMap3D

:: DESCRIPTION

InterMap3D predicts interacting protein residues by identifying co-evolving pairs of aminoacids from an alignment of protein sequences.

::DEVELOPER

Stockholm Bioinformatics Center

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

InterMap3D: predicting and visualizing co-evolving protein residues.
Gouveia-Oliveira R, Roque FS, Wernersson R, Sicheritz-Ponten T, Sackett PW, Mølgaard A, Pedersen AG.
Bioinformatics. 2009 Aug 1;25(15):1963-5. doi: 10.1093/bioinformatics/btp335.

BinMemPredict – Predicting Membrane Protein Types

BinMemPredict

:: DESCRIPTION

BinMemPredict is a platform that supports users to submit multiple sequences for prediction at one time. It offers two kinds of features to train model, one of which is 20-D feature based on PSSM matrix and the other is 188-D feature based on the composition and physical-chemical properties.

::DEVELOPER

Data Mining Group, Xiamen University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • JAVA

:: DOWNLOAD

 BinMemPredict

:: MORE INFORMATION

Citation

Quan Zou, Xubin Li, Yi Jiang, Yuming Zhao, Guohua Wang.
BinMemPredict: a Web server and software for predicting membrane protein types.
Current Proteomics. 2013, 10(1): 2-9

zqFold – Predicting RNA Secondary Structure

zqFold

:: DESCRIPTION

zqFold is a simple software for predicting RNA secondary structure. The most development from RNAstructure is that it can predict based on species. For example, if you choose ‘tRNA’, and the sequence will be folded as a cloverleaf; if you choose ‘siRNA’ or ‘microRNA precursor’, it will be folded as a hairpin.

::DEVELOPER

Dr. Quan Zou , Tuo Zhao ,

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows
  • JRE

:: DOWNLOAD

 zqFold

:: MORE INFORMATION

Citation

Quan Zou, Tuo Zhao, Yang Liu, Maozu Guo.
Predicting RNA secondary structure based on the class information and Hopfield network.
Computers in Biology and Medicine. 2009,39(3):206-214

Signal-CF – Predicting Signal Peptides

Signal-CF

:: DESCRIPTION

Signal-CF is an automated method for predicting signal peptide sequences and their cleavage sites in eukaryotic and bacterial protein sequences

::DEVELOPER

Computational Systems Biology Group, Shanghai Jiao Tong University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

Biochem Biophys Res Commun. 2007 Jun 8;357(3):633-40. Epub 2007 Apr 5.
Signal-CF: a subsite-coupled and window-fusing approach for predicting signal peptides.
Chou KC1, Shen HB.