CorrDCA
Warning
DISCONTINUED in favor of DCAUtils.jl
Intro
Simple package that:
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Reads FASTA files and translate it in a numerical matrix
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Computes the reweighting score as described in "Fast and accurate multivariate Gaussian modeling of protein families: Predicting residue contacts and protein-interaction partners" by Carlo Baldassi, Marco Zamparo, Christoph Feinauer, Andrea Procaccini, Riccardo Zecchina, Martin Weigt and Andrea Pagnani, (2014) PLoS ONE 9(3): e92721. doi:10.1371/journal.pone.0092721
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Compute empirical frequency counts (with and without pseudocount)
Usage
The computation of the sequence weights is typically very expensive computationaly. A considerable speed-up can be achieved by exploiting parallel computation. To do so, just start julia with the -p nprocs argument where nprocs is the number of workers available on your machine. Alternatively, from julia REPL, just do a:
julia> using Distributed;
julia> addprocs(8) # put here the number of cores available
julia> @everywhere using CorrDCA
Credits
All methods available here are present also in the (so far) unregistered "GaussDCA" package.
The remove_duplicate_sequences has been basically copied by it.