Code and data for "A new selective force driving metabolic genes clustering"

Description

Here we store code and ideas related to our collaborative project on describing Operon Evolution by the integration of systems biology and comparative genomics tools. The question of interest is how the position of genes can be selected for such that on the long time gene clusters and then operons can form. Advantages provided by the operon have been discussed since long, but they only explain why once an operon has been formed, it is kept. what about the driving force enabling genes to get close such that an operon can form? This is a very different question. In this work we propose that a reasonable driving force comes from the perturbations to metabolic homeostasis that are consequent to an active replication of the chromosome. We provide theoretical evidence by combining DNA replication with Metabolic Control Theory and find support by exploiting both simulations and more importantly, comparative genomics analysis.

Steps to reproduce

RData, txt, csv files contains data used by one or more of the scripts, therefore we suggest to leave everything in the same folder. Scripts are for R (.R) or Matlab (.m). They are commented and easy to run once the required dependencies are installed. The linlog,zip archive contains data for reproducing both the optimization of gene positions and the simulation dealing with the structural rearrangements explicitly. Everything with no .R extension contain data, in some case redundant. For instance the metabolic model is stored in the RData file, but its parameters can also be found in text files. The .R script, at present directly loads the RData file. For any problem, mail to matteo.brilli (at) unimi.it

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