NetCoffee specifications

Information


Unique identifier OMICS_05172
Name NetCoffee
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages C++
License GNU General Public License version 3.0, GNU General Public License version 2.0
Computer skills Advanced
Stability Stable
Maintained Yes

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Documentation


Maintainer


  • person_outline Xuequn Shang <>

Additional information


http://www.nwpu-bioinformatics.com/WebNetCoffee/help.php

Information


Unique identifier OMICS_05172
Name NetCoffee
Interface Web user interface
Restrictions to use Academic or non-commercial use
Programming languages C++
License GNU General Public License version 3.0
Computer skills Basic
Stability Stable
Maintained Yes

Documentation


Maintainer


  • person_outline Xuequn Shang <>

Additional information


http://www.nwpu-bioinformatics.com/WebNetCoffee/help.php

Publications for NetCoffee

NetCoffee in publications

 (2)
PMCID: 5270500
PMID: 28194172
DOI: 10.1186/s13637-015-0022-9

[…] edges between each pair of cliques, and repeatedly merges the cliques to form aligned node clusters until the alignment score (with respect to edge conservation) can no longer be maximized. netcoffee’s [] cost function is based on the likelihood that two given proteins (from different networks) are topologically conserved. its alignment strategy constructs a weighted bipartite graph […]

PMCID: 4331682
PMID: 25707987
DOI: 10.1186/1752-0509-9-S1-S7

[…] scores using a semi-markov random walk model, and then uses the estimated scores to predict the maximum expected accuracy (mea) alignment of the given networks. given a set of networks, netcoffee [] generates all possible combinations of bipartite graphs for these networks, and updates the edges in each bipartite graph based on the sequence similarity of the proteins […]


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NetCoffee institution(s)
School of Computer Science, Northwestern Polytechnical University, Xi’an, China; Centre for Multidisciplinary Convergence Computing, School of Computer Science, Northwestern Polytechnical University, Xi’an, China
NetCoffee funding source(s)
Supported by the National Natural Science Foundation of China (Grant No. 61702420); by the National Natural Science Foundation of China (Grant No. 61332014, 61702420 and 61772426); the China Postdoctoral Science Foundation (Grant No. 2017M613203); the Natural Science Foundation of Shaanxi Province (Grant No. 2017JQ6037); the Fundamental Research Funds for the Central Universities (Grant No. 3102018zy032).

NetCoffee review

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Anonymous user #973

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It's the-state-of-the-art algorithm for the multiple network alignment problem. Fast, Scalable, and Accurate!