WebNetCoffee: a web-based application to identify functionally conserved proteins from Multiple PPI networks
Abstract Background The 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...
| Main Authors: | , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2018-11-01
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| Series: | BMC Bioinformatics |
| Subjects: | |
| Online Access: | http://link.springer.com/article/10.1186/s12859-018-2443-4 |
| _version_ | 1818084767191531520 |
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| author | Jialu Hu Yiqun Gao Junhao He Yan Zheng Xuequn Shang |
| author_facet | Jialu Hu Yiqun Gao Junhao He Yan Zheng Xuequn Shang |
| author_sort | Jialu Hu |
| collection | DOAJ |
| description | Abstract Background The 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. Results Here, 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. Conclusion WebNetCoffee 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 |
| first_indexed | 2024-12-10T19:59:07Z |
| format | Article |
| id | doaj.art-8bbea6d31f214366a3333e6ff89bb034 |
| institution | Directory Open Access Journal |
| issn | 1471-2105 |
| language | English |
| last_indexed | 2024-12-10T19:59:07Z |
| publishDate | 2018-11-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Bioinformatics |
| spelling | doaj.art-8bbea6d31f214366a3333e6ff89bb0342022-12-22T01:35:35ZengBMCBMC Bioinformatics1471-21052018-11-011911610.1186/s12859-018-2443-4WebNetCoffee: a web-based application to identify functionally conserved proteins from Multiple PPI networksJialu Hu0Yiqun Gao1Junhao He2Yan Zheng3Xuequn Shang4School of Computer Science, Northwestern Polytechnical UniversitySchool of Computer Science, Northwestern Polytechnical UniversitySchool of Computer Science, Northwestern Polytechnical UniversitySchool of Computer Science, Northwestern Polytechnical UniversitySchool of Computer Science, Northwestern Polytechnical UniversityAbstract Background The 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. Results Here, 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. Conclusion WebNetCoffee 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/WebNetCoffeehttp://link.springer.com/article/10.1186/s12859-018-2443-4Multiple network alignmentWebserverPPI networksProtein databasesGene ontology |
| spellingShingle | Jialu Hu Yiqun Gao Junhao He Yan Zheng Xuequn Shang WebNetCoffee: a web-based application to identify functionally conserved proteins from Multiple PPI networks BMC Bioinformatics Multiple network alignment Webserver PPI networks Protein databases Gene ontology |
| title | WebNetCoffee: a web-based application to identify functionally conserved proteins from Multiple PPI networks |
| title_full | WebNetCoffee: a web-based application to identify functionally conserved proteins from Multiple PPI networks |
| title_fullStr | WebNetCoffee: a web-based application to identify functionally conserved proteins from Multiple PPI networks |
| title_full_unstemmed | WebNetCoffee: a web-based application to identify functionally conserved proteins from Multiple PPI networks |
| title_short | WebNetCoffee: a web-based application to identify functionally conserved proteins from Multiple PPI networks |
| title_sort | webnetcoffee a web based application to identify functionally conserved proteins from multiple ppi networks |
| topic | Multiple network alignment Webserver PPI networks Protein databases Gene ontology |
| url | http://link.springer.com/article/10.1186/s12859-018-2443-4 |
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