Tag: Matrix

MIA – Matrix Integrative Analysis

MIA

:: DESCRIPTION

MIA is a MATLAB package, implementing and extending four computational methods (Guide). MIA can integrate diverse types of genomic data (e.g., copy number variation, DNA methylation, gene expression, microRNA expression profiles and/or gene network data) to identify the underlying modular patterns. MIA is flexible and can handle a wide range of biological problems and data types.

::DEVELOPER

Shihua Zhang’s Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux
  • MatLab

:: DOWNLOAD

MIA

:: MORE INFORMATION

Citation

Chen J, Zhang S.
Matrix Integrative Analysis (MIA) of Multiple Genomic Data for Modular Patterns.
Front Genet. 2018 May 29;9:194. doi: 10.3389/fgene.2018.00194. PMID: 29910825; PMCID: PMC5992392.

iONMF 1.1 – Integrative Orthogonal Non-negative Matrix Factorization

iONMF 1.1

:: DESCRIPTION

iONMF is an integrative approach to model and predict multiple data sources based on orthogonal matrix factorization.

::DEVELOPER

BioLab , University of Ljubljana

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 iONMF

:: MORE INFORMATION

Citation

Orthogonal matrix factorization enables integrative analysis of multiple RNA binding proteins.
Stražar M, Žitnik M, Zupan B, Ule J, Curk T.
Bioinformatics. 2016 Jan 18. pii: btw003

RaPPer – Generate Random perfect Phylogeny Matrix

RaPPer

:: DESCRIPTION

RaPPer will generate random perfect phylogeny matrix with following conditions.

::DEVELOPER

School of Biological Sciences, Iran

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/ Linux / MacOsX
  • MatLab

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Adv Appl Bioinform Chem. 2010;3:89-96. doi: 10.2147/AABC.S13397. Epub 2010 Nov 16.
Construction of random perfect phylogeny matrix.
Sadeghi M1, Pezeshk H, Eslahchi C, Ahmadian S, Abadi SM.

PAUL 2.0 – Protein Distance Matrix Alignment

PAUL 2.0

:: DESCRIPTION

PAUL (Protein Alignment Using Lagrangian relaxation) is a tool for the computation of protein structure alignments based on sparse protein distance matrices

::DEVELOPER

Life Sciences Group, Centrum Wiskunde & Informatica

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • T-Coffee

:: DOWNLOAD

 PAUL

:: MORE INFORMATION

Citation

Bioinformatics. 2010 Sep 15;26(18):2273-80. doi: 10.1093/bioinformatics/btq420. Epub 2010 Jul 17.
Towards optimal alignment of protein structure distance matrices.
Wohlers I1, Domingues FS, Klau GW.

FitchAln 20100321 – Given Phylogenetic Tree and Multiple Sequence Alignment, show the Fitch Score Matrix

FitchAln 20100321

:: DESCRIPTION

Given a newick binary tree T and its correpsonding multiple sequence alignemnt A of size n x m, where n is the number of leaf nodes in T and m is the length of the alignment, FitchAln generates a (n-1) x (m+1) Fitch score matrix representing the (Maximum Parsimony) number of mutations for each site for each internal node.

::DEVELOPER

UCF Computational Biology and Bioinformatics Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C Compiler

:: DOWNLOAD

 FitchAln

:: MORE INFORMATION

AutoMatrix – Calculate an Instantaneous Rate Matrix

AutoMatrix

:: DESCRIPTION

AutoMatrix is a Matlab script that will calculate an instantaneous rate matrix (and its eigen value decompostion for use in phylip programs) from a series of substitution count matrices calculated for different levels of sequence identity/similarity.

::DEVELOPER

The Tillier Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • MatLab

:: DOWNLOAD

 AutoMatrix

:: MORE INFORMATION

Citation:

A transition probability model for amino acid substitutions from BLOCKS
Shalini Veerassamy, Andrew Smith and Elisabeth R. M. Tillier,
J. Computational Biology (2003) 10(6): 997-1010

DistMiss 1.0 – Compute Matrix of Genetic Distances between Populations

DistMiss 1.0

:: DESCRIPTION

DistMiss computes a matrix of genetic distances between populations on the basis of their allele frequencies at L loci.

::DEVELOPER

DistMiss Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows
  • Fortran

:: DOWNLOAD

 DistMiss

:: MORE INFORMATION

PMSearch – Poly Matrix Search

PMSearch

:: DESCRIPTION

PMSearch (Poly Matrix Search) is a tool that utilizes Position Weight Matrices to search for putative Transcription Factor Binding Sites. PMSearch takes Position Frequency Matrices (PFMs) and DNA sequences to initiate a prediction task. The user may upload motifs/matrices (Position Frequency Matrices, PFM or Position Weight Matrices, PWM))or retrieve PFMs from our local dataset as input. We currently have 507 PFMs downloaded from Transfac Public Database 7.0 and JASPAR. Besides PFMs, the user may add multiple sequences in FASTA or Genbank format. PMSearch outputs a plot, a table of location, score and motif of each high scoring site and clusters of these sites.

::DEVELOPER

Bioinformatics Group in Nanjing University.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Bioinformation. 2006 Jun 15;1(5):156-7.
A web server for transcription factor binding site prediction.
Su G, Mao B, Wang J.

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