Codebase for Direct Coupling Analysis applied to nucleotide recognition
This package contains codes specific for DCA-scape analysis:
1. masterDCAparameters_length - estimating the mean couplings and local field parameters from the input nucleotide fasta data for each
of the four nucleotides gauged states.
2.Fastahamiltonian - Calculating the Hamiltonian score for any 20mer sequences list base on the average couplings and local fields.
Lambda genome sequence fasta file (lamdba_genome_seq.fasta) is provided as an example for the Hamiltonian score calculation.
All of these codes are based on MATLAB. Below is one example for the basic analysis of lambda SEQRS data.
[c_average,h_average] = masterDCAparameters_length('RPI_033_lambda.fasta',20); [c_average_GST,h_average_GST] = masterDCAparameters_length('RPI_033_GST_lambda.fasta',20);
Hamiltonian_score_033=Fastahamiltonian('lambda_genome_seq.fasta',c_average_033,h_average_033,2,0,2); Hamiltonian_score_gst=Fastahamiltonian('lambda_genome_seq.fasta',c_average_031_GST,h_average_031_GST,2,0,2);
Hamiltonian_score_033_gst=Hamiltonian_score_033-Hamiltonian_score_gst;
Any publication resulting from applications of DCA-scapes should cite:
Q Zhou, N Kunder, Jose Alberto De la Paz, AE. Lasley, VD.Bhat, F Morcos, ZT. Campbell (2018), Global pairwise RNA interaction landscapes reveal corefeatures of protein recognition.
Q Zhou, A D Stanowick1, J A de la Paz, X Lin, F Morcos (2025) Characterizing DNA Recognition Preferences of Transcription Factors Using Global Couplings and High-throughput Sequencing (in preparation)