Alignment of biological networks by integer linear programming: virus-host protein-protein interaction networks
Background: The alignment of protein-protein interaction networks was recently formulated as an integer quadratic programming problem, along with a linearization that can be solved by integer linear programming software tools. However, the resulting integer linear program has a huge number of variab...
| Autores: | , , , |
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| Tipo de recurso: | artículo |
| Fecha de publicación: | 2020 |
| País: | España |
| Institución: | Universitat Politècnica de Catalunya (UPC) |
| Repositorio: | UPCommons. Portal del coneixement obert de la UPC |
| Idioma: | inglés |
| OAI Identifier: | oai:upcommons.upc.edu:2117/334544 |
| Acceso en línea: | https://hdl.handle.net/2117/334544 https://dx.doi.org/10.1186/s12859-020-03733-w |
| Access Level: | acceso abierto |
| Palabra clave: | Computational biology Protein research Systems biology Virus-host protein-protein interaction Integer linear programming Network alignment Graph matching Biologia computacional Programació en nombres enters Proteïnes -- Investigació Àrees temàtiques de la UPC::Informàtica::Aplicacions de la informàtica::Bioinformàtica |
| Sumario: | Background: The alignment of protein-protein interaction networks was recently formulated as an integer quadratic programming problem, along with a linearization that can be solved by integer linear programming software tools. However, the resulting integer linear program has a huge number of variables and constraints, rendering it of no practical use. Results: We present a compact integer linear programming reformulation of the protein-protein interaction network alignment problem, which can be solved using state-of-the-art mathematical modeling and integer linear programming software tools, along with empirical results showing that small biological networks, such as virus-host protein-protein interaction networks, can be aligned in a reasonable amount of time on a personal computer and the resulting alignments are structurally coherent and biologically meaningful. Conclusions: The implementation of the integer linear programming reformulation using current mathematical modeling and integer linear programming software tools provided biologically meaningful alignments of virus-host protein-protein interaction networks. |
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