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Protein Networks02:26

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When solving problems using the energy conservation law, the object (system) to be studied should first be identified. Often, in applications of energy conservation, we study more than one body at the same time. Second, identify all forces acting on the object and determine whether each force doing work is conservative. If a non-conservative force (e.g., friction) is doing work, then mechanical energy is not conserved. The system must then be analyzed with non-conservative work. Third, for...
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WebNetCoffee: a web-based application to identify functionally conserved proteins from Multiple PPI networks.

Jialu Hu1,2, Yiqun Gao1, Junhao He1

  • 1School of Computer Science, Northwestern Polytechnical University, Xi'an, 710072, China.

BMC Bioinformatics
|November 14, 2018
PubMed
Summary
This summary is machine-generated.

WebNetCoffee is a novel web server for global multiple protein-protein interaction (PPI) network alignment. It enables users to analyze their own data and discover functionally conserved proteins across networks.

Keywords:
Gene ontologyMultiple network alignmentPPI networksProtein databasesWebserver

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Area of Science:

  • Systems biology
  • Bioinformatics
  • Computational biology

Background:

  • Identifying functionally conserved proteins is crucial in systems biology.
  • Global network alignment of protein-protein interaction (PPI) networks is a key strategy for this discovery.
  • Existing tools lack the capability for multiple PPI network alignment on user-defined datasets.

Purpose of the Study:

  • To develop a web server, WebNetCoffee, for performing global multiple network alignment.
  • To provide a platform for analyzing user-submitted datasets and publicly available data.

Main Methods:

  • Developed the WebNetCoffee web server utilizing the NetCoffee algorithm.
  • Compiled extensive online datasets including 218,339 proteins and 4,009,541 interactions from public databases.
  • Integrated features for job management and visualization of alignment results.

Main Results:

  • Successfully created WebNetCoffee, a web server for global multiple PPI network alignment.
  • Assembled comprehensive online test datasets for user analysis and algorithm comparison.
  • Made all datasets and alignment results downloadable for further research.

Conclusions:

  • WebNetCoffee offers a user-friendly interface for global alignment of multiple PPI networks.
  • It is the first web server to support global alignment tasks on user-submitted datasets.
  • The server facilitates the visualization of protein subnetworks and supports downstream analyses.