DegSampler2

  Matlab code of DegSampler2

inputseqsets


RocSampler

readme.txt

help.txt

RocSampler

 

It can be executed in a Cygwin terminal with the following command:

RocSampler ppi-file output-file [options].

 

Citation: Osamu Maruyama and Yuki Kuwahara, RocSampler: Regularizing Overlapping Protein Complexes in Protein-Protein Interaction Networks, to appear.


PPSampler2 tool for predicting protein complexes by sampling

 

   Version 2.3:

            readme.txt

            PPSampler2.exe

 

            Whats new? The following two options are available:

 

    --f1DenominatorExponent <exponent>

        set the exponent of the denominator of f1(c), where c is a cluster,

        to be <exponent>. The default is 0.5.

    --f2

        add the function, f2, into the whole scoring function, f. Without this

        option, f2 is not included in f. In the default, this option is not valid.

 

   Version 2.2:

readme.txt

PPSampler2.exe

 

Verify the MATLAB Compiler Runtime (MCR) is installed and ensure you have installed version 8.2 (R2013b).  

MCR will be found in http://www.mathworks.com/products/compiler/mcr/index.html.

 

Citation: Chasanah Kusumastuti Widita and Osamu Maruyama, PPSampler2: Predicting protein complexes more accurately and efficiently by sampling, BMC Systems Biology, 7(Suppl 6):S14, 2013.


PPSampler tool for predicting protein complexes by sampling

readme.txt

PPSamplerVer1.2.exe

Verify the MATLAB Compiler Runtime (MCR) is installed and ensure you have installed version 8.1 (R2013a).  

MCR will be found in http://www.mathworks.com/products/compiler/mcr/index.html.

 

Citation: Daisuke Tatsuke and Osamu Maruyama, Sampling strategy for protein complex prediction using cluster size frequency, Gene, 518(1), 152-158, 2012.


Naïve Bayes classifier for Heterodimeric protein complex prediction:

README.txt (updated at 07/08/2014)

The main program (jar file) is NBC-HD-PCP.jar. (updated at 07/08/2014)

features.txt specifies the names of features embedded into naïve Bayes classifiers.

Input data files can be found in data_files.zip.

 

Citation: Osamu Maruyama, Heterodimeric Protein Complex Identification by Naïve Bayes Classifiers, BMC Bioinformatics, 14:347, 2013.


NWE Node weighted expansion for predicting protein complexes by random walks with restarts

  NWE.zip

Citation: Osamu Maruyama and Ayaka Chihara, NWE: Node-weighted expansion for protein complex prediction using random walk distances, Proteome Science, 9(Suppl 1):S14, 2011.


Motif-Finder SUPERPOSITION

SUPERPOSITION is a program which finds pattern over IUPAC nucleic acid codes, conserved in a given set of DNA sequences.

version 01 (changes)