DegSampler
The version 2.3 of DegSampler is available.
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:
What’s 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:
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
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
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.
SUPERPOSITION is a program which finds pattern over IUPAC nucleic acid codes, conserved in a given set of DNA sequences.