MIDER v2 – Mutual Information Distance and Entropy Reduction

MIDER v2

:: DESCRIPTION

MIDER is a general purpose software tool for inferring network structures. It has been developed with biological networks in mind, but can be applied in other areas.

::DEVELOPER

(Bio)Process Engineering group, IIM-CSIC

:: SCREENSHOTS

MIDER

:: REQUIREMENTS

  • Linux /Windows/MacOsX
  • MatLab

:: DOWNLOAD

 MIDER

:: MORE INFORMATION

Citation

MIDER: Network Inference with Mutual Information Distance and Entropy Reduction.
Villaverde AF, Ross J, Morán F, Banga JR.
PLoS One. 2014 May 7;9(5):e96732. doi: 10.1371/journal.pone.0096732. eCollection 2014.

GIREMI – Genome-independent Identification of RNA Editing by Mutual Information

GIREMI

:: DESCRIPTION

GIREMI is a method that can identify RNA editing sites using one RNA-seq data set without requiring genome sequence data.

::DEVELOPER

XIAO LAB

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl
  • R
  • C++ Compiler

:: DOWNLOAD

 GIREMI

:: MORE INFORMATION

Citation:

Nat Methods. 2015 Mar 2. doi: 10.1038/nmeth.3314.
Genome sequence-independent identification of RNA editing sites.
Zhang Q, Xiao X

MISTIC – Mutual Information Server to Infer Coevolution

MISTIC

:: DESCRIPTION

MISTIC is a web server for graphical representation of the information contained within a MSA (multiple sequence alignment) and a complete analysis tool for Mutual Information networks in protein families.

::DEVELOPER

Structural Bioinformatics Unit, Fundación Instituto Leloir

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2013 Jul;41(Web Server issue):W8-14. doi: 10.1093/nar/gkt427. Epub 2013 May 28.
MISTIC: Mutual information server to infer coevolution.
Simonetti FL1, Teppa E, Chernomoretz A, Nielsen M, Marino Buslje C.

iPAGE 1.2a – Functional and Categorical Enrichment program based on Mutual information

iPAGE 1.2a

:: DESCRIPTION

iPAGE is a powerful package which in conjunction with FIRE provides a complete meta-analysis of whole-genome datasets.

::DEVELOPER

Tavazoie lab at Columbia University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ MacOsX
  • Perl

:: DOWNLOAD

 iPAGE

:: MORE INFORMATION

Citation:

Mol Cell. 2009 Dec 11;36(5):900-11. doi: 10.1016/j.molcel.2009.11.016.
Revealing global regulatory perturbations across human cancers.
Goodarzi H, Elemento O, Tavazoie S.

FIRE-pro 1.1 – Motif Discovery and Characterization program in Proteins based on Mutual Information

FIRE-pro 1.1

:: DESCRIPTION

FIRE-pro (Finding Informative Regulatory Elements in proteins) is a motif discovery and characterization program for proteins based on mutual information

::DEVELOPER

Tavazoie lab at Columbia University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ MacOsX / Windows
  • Perl

:: DOWNLOAD

 FIRE-pro

:: MORE INFORMATION

Citation:

PLoS One. 2010 Dec 29;5(12):e14444. doi: 10.1371/journal.pone.0014444.
Large-scale discovery and characterization of protein regulatory motifs in eukaryotes.
Lieber DS, Elemento O, Tavazoie S.

FIRE 1.1a – Motif Discovery and Characterization program based on Mutual Information

FIRE 1.1a

:: DESCRIPTION

FIRE (Finding Informative Regulatory Elements) is a motif discovery and characterization program based on mutual information

::DEVELOPER

Tavazoie lab at Columbia University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ MacOsX / Windows
  • Perl

:: DOWNLOAD

 FIRE

:: MORE INFORMATION

Citation:

Mol Cell. 2007 Oct 26;28(2):337-50.
A universal framework for regulatory element discovery across all genomes and data types.
Elemento O, Slonim N, Tavazoie S.

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.