:: DESCRIPTION
PANDA (Propagation of Affinity and Domain Architecture) is a web server to predict protein functions in the format of Gene Ontology (GO) terms.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Wang Z, Zhao C, Wang Y, Sun Z, Wang N.
PANDA: Protein function prediction using domain architecture and affinity propagation.
Sci Rep. 2018 Feb 22;8(1):3484. doi: 10.1038/s41598-018-21849-1. PMID: 29472600; PMCID: PMC5823857.
:: DESCRIPTION
WebPropagate is a web-server that implements variants of network propagation on up-to-date PPI networks. Starting from a seed set of proteins that are known to be associated with a process of interest, WebPropagate outputs additional candidate proteins that are significantly associated with the seed set.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
WebPropagate: A Web Server for Network Propagation.
Biran H, Almozlino T, Kupiec M, Sharan R.
J Mol Biol. 2018 Jul 20;430(15):2231-2236. doi: 10.1016/j.jmb.2018.02.025.
:: DESCRIPTION
PRINCE (PRIoritizatioN and Complex Elucidation) is a method for prioritizing disease associated genes.PRINCIPLE (PRINCe ImPLEmentation) is a client-server implementation of PRINCE
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Bioinformatics. 2011 Dec 1;27(23):3325-6. doi: 10.1093/bioinformatics/btr584. Epub 2011 Oct 20.
PRINCIPLE: a tool for associating genes with diseases via network propagation.
Gottlieb A1, Magger O, Berman I, Ruppin E, Sharan R.
:: DESCRIPTION
The apcluster package implements Frey’s and Dueck’s Affinity Propagation clustering in R. The algorithms are largely analogous to the Matlab code published by Frey and Dueck. The package further provides an algorithm for exemplar-based agglomerative clustering that can also be used to join clusters obtained from affinity propagation. Various plotting functions are available for analyzing clustering results
::DEVELOPER
Institute of Bioinformatics, Johannes Kepler University Linz
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
U. Bodenhofer, A. Kothmeier, and S. Hochreiter (2011).
APCluster: an R package for affinity propagation clustering.
Bioinformatics 27:2463-2464
:: DESCRIPTION
The FunCProp project applies novel label propagation techniques to many different types of gene and protein data in order to predict protein function via Gene Ontology annotations.
::DEVELOPER
the Bonneau Lab
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Bioinformatics. 2013 May 1;29(9):1190-8. doi: 10.1093/bioinformatics/btt110. Epub 2013 Mar 19.
Parametric Bayesian priors and better choice of negative examples improve protein function prediction.
Youngs N, Penfold-Brown D, Drew K, Shasha D, Bonneau R.
