Paper: Engineering repressors with coevolutionary cues facilitates toggle switches with a master reset Authors: Rey P. Dimas, Xian-Li Jiang, Jose Alberto de la Paz, Faruck Morcos, Clement T. Y. Chan Description: This README file describes the data package and code accompanying the above publication. Files: MSA_LacI_homologs: fasta file, contains the multiple sequence alignments for 74,287 LacI homologs. The sequences are obtained from Uniprot database by using the hmm profile of LacI with the command hmmsearch. lacI_eij_hi_parameters: MAT file, contains the pairwise coupling and local fields parameters. They are computed from about 70,000 LacI homologs by DCA method (DCAparameters.m). It can be read by MATLAB. LacI family residue pairs with top 1500 DI values: Txt file, contains strongly coevolved residue pairs between DNA recognition module and environmental sensing module. Their direct information values are computed by DCA method (dca.m) and are among the top 1500. The original dca code can be found in dca.rice.edu. 8_LacI_homolgs_shuffled_at_47: fasta file, contains the multiple sequence alignment of CelR, GalR, LacI, MalR, RbsR, ScrR, XltR, and PurR native sequences and hybrid sequences. The hybrids are generate by shuffling at the homologous position of LacI 47. All the codes and MATLAB data file are ran and open by the software MATLAB, which can be downloaded from: https://www.mathworks.com/products/matlab.html . Steps: 1. MSA_LacI_homologs.fasta and DCAparameters.m: Generate the parameters (as in lacI_eij_hi_parameters.mat) by using the DCAparameters.m code in the following link: http://morcoslaboratory.org/?page_id=385 . 2. MSA_LacI_homologs.fasta and dca.m: Calculate the pairwise direct information (DI) values by using the dca.m code in the following link: http://dca.rice.edu/portal/dca/ Sort the pairs with inclusion of only inter-module pairs, select top 1500 pairs. Generate the file LacI family residue pairs with top 1500 DI values.txt 3. 3 files are used to calculate the compatibility score: LacI family residue pairs with top 1500 DI values.txt lacI_eij_hi_parameters.mat 8_LacI_homolgs_shuffled_at_47.txt