Similar protocols

Pipeline publication

[…] m and comparing the obtained network performance to the one obtained in the original environment., Detail of the algorithms for in silico analyses can be found in the Supplementary Note ; scripts are freely available and can be downloaded at the following location (http://lipm-bioinfo.toulouse.inra.fr/systemsbiology/models/rsolanacearum)., Homology groups of proteins sequences in 29 bacterial genomes downloaded on NCBI database (see Supplementary Table  for the list) were assigned using OrthoMCL via Family-Companion (http://family-companion.toulouse.inra.fr). Sequence clustering was performed using a p-value cut-off of 1 × 10−5, and a percent match cut-off of 80. Sequences were aligned with Mafft v7.271. Columns with more than 50% of gaps were removed. Phylogenetic trees were computed with IQ-tree (automatic mode) and drawn with Itol (https://itol.embl.de/)., The BECO method is available in the FlexFlux library (http://lipm-bioinfo.toulouse.inra.fr/flexflux/documentation.html#beco). Codes for VRN validation are available from the corresponding author upon request., The data that support the findings of this study are available in the website dedicated to the cell model of Ralstonia solanacearum (http://lipm-bioinfo.toulouse.inra.fr/systemsbiology/models/rsolanacearum/download.html). The metabolic network is available in BioModels with the identifier MODEL1612020000. The VRN model was deposited also in BioModels and assigned the identifier MODEL1710170000., , Electronic supplementary material , Supple […]

Pipeline specifications

Software tools MAFFT, IQ-TREE, iTOL
Organisms Bacteria
Diseases Infection