Iñigo Apaolaza1, Luis Vitores Valcarcel1,2, Francisco J Planes1. 1. Department of Biomedical Engineering and Sciences, Tecnun School of Engineering, University of Navarra, San Sebastián, Spain. 2. Centro de Investigación Médica Aplicada (CIMA), University of Navarra, Programa de Oncohematología, Pamplona, Spain.
Abstract
Motivation: The identification of minimal gene knockout strategies to engineer metabolic systems constitutes one of the most relevant applications of the COnstraint-Based Reconstruction and Analysis (COBRA) framework. In the last years, the minimal cut sets (MCSs) approach has emerged as a promising tool to carry out this task. However, MCSs define reaction knockout strategies, which are not necessarily transformed into feasible strategies at the gene level. Results: We present a more general, easy-to-use and efficient computational implementation of a previously published algorithm to calculate MCSs to the gene level (gMCSs). Our tool was compared with existing methods in order to calculate essential genes and synthetic lethals in metabolic networks of different complexity, showing a significant reduction in model size and computation time. Availability and implementation: gMCS is publicly and freely available under GNU license in the COBRA toolbox (https://github.com/opencobra/cobratoolbox/tree/master/src/analysis/gMCS). Supplementary information: Supplementary data are available at Bioinformatics online.
Motivation: The identification of minimal gene knockout strategies to engineer metabolic systems constitutes one of the most relevant applications of the COnstraint-Based Reconstruction and Analysis (COBRA) framework. In the last years, the minimal cut sets (MCSs) approach has emerged as a promising tool to carry out this task. However, MCSs define reaction knockout strategies, which are not necessarily transformed into feasible strategies at the gene level. Results: We present a more general, easy-to-use and efficient computational implementation of a previously published algorithm to calculate MCSs to the gene level (gMCSs). Our tool was compared with existing methods in order to calculate essential genes and synthetic lethals in metabolic networks of different complexity, showing a significant reduction in model size and computation time. Availability and implementation: gMCS is publicly and freely available under GNU license in the COBRA toolbox (https://github.com/opencobra/cobratoolbox/tree/master/src/analysis/gMCS). Supplementary information: Supplementary data are available at Bioinformatics online.
Authors: Iñigo Apaolaza; Edurne San José-Enériz; Luis V Valcarcel; Xabier Agirre; Felipe Prosper; Francisco J Planes Journal: PLoS Comput Biol Date: 2022-03-14 Impact factor: 4.475