GEMtractor: extracting views into genome-scale metabolic models | Zendy

Martin Scharm | Zendy; Olaf Wolkenhauer | Zendy; Mahdi Jalili | Zendy; Ali SalehzadehYazdi | Zendy

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GEMtractor: extracting views into genome-scale metabolic models

Author(s) -

Martin Scharm,

Olaf Wolkenhauer,

Mahdi Jalili,

Ali SalehzadehYazdi

Publication year - 2020

Publication title -

bioinformatics

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 3.599

H-Index - 390

eISSN - 1367-4811

pISSN - 1367-4803

DOI - 10.1093/bioinformatics/btaa068

Subject(s) - sbml , computer science , encode , theoretical computer science , multipartite , genome , markup language , biology , world wide web , genetics , xml , gene , physics , quantum mechanics , quantum entanglement , quantum

Computational metabolic models typically encode for graphs of species, reactions and enzymes. Comparing genome-scale models through topological analysis of multipartite graphs is challenging. However, in many practical cases it is not necessary to compare the full networks. The GEMtractor is a web-based tool to trim models encoded in SBML. It can be used to extract subnetworks, for example focusing on reaction- and enzyme-centric views into the model.

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