ArticleBMC bioinformatics2018
WebNetCoffee: a web-based application to identify functionally conserved proteins from Multiple PPI networks.
Article in BMC bioinformatics, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.
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Who cites it
3 citing papers in PubMed.
- A novel algorithm for alignment of multiple PPI networks based on simulated annealing.BMC genomics · 2019Article
- A novel algorithm based on bi-random walks to identify disease-related lncRNAs.BMC bioinformatics · 2019Article
- MD-SVM: a novel SVM-based algorithm for the motif discovery of transcription factor binding sites.BMC bioinformatics · 2019Article
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Authors and funding
5 authors.
Funding
Abstract
backgroundThe discovery of functionally conserved proteins is a tough and important task in system biology. Global network alignment provides a systematic framework to search for these proteins from multiple protein-protein interaction (PPI) networks. Although there exist many web servers for network alignment, no one allows to perform global multiple network alignment tasks on users' test datasets.
resultsHere, we developed a web server WebNetcoffee based on the algorithm of NetCoffee to search for a global network alignment from multiple networks. To build a series of online test datasets, we manually collected 218,339 proteins, 4,009,541 interactions and many other associated protein annotations from several public databases. All these datasets and alignment results are available for download, which can support users to perform algorithm comparison and downstream analyses.
conclusionWebNetCoffee provides a versatile, interactive and user-friendly interface for easily running alignment tasks on both online datasets and users' test datasets, managing submitted jobs and visualizing the alignment results through a web browser. Additionally, our web server also facilitates graphical visualization of induced subnetworks for a given protein and its neighborhood. To the best of our knowledge, it is the first web server that facilitates the performing of global alignment for multiple PPI networks. AVAILABILITY: http://www.nwpu-bioinformatics.com/WebNetCoffee.
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