Pre-requisite:
Python3.6+ and packages:
pandas
numpy
tqdm
There is one executable in Src/: dca_protrna.py
usage: dca_protrna.py [-h] --input INPUT [--output OUTPUT] [--nprocs NPROCS]
[--gaps GAPS] [--conservation CONSERVATION]
Mandatory option:
--input -i An fasta-ish input file. Every sequence must have a title starting with ">"
The following line has a protein sequence followed by an RNA sequence, white spaces in between (space or tabs)
Gaps MUST BE dots '.'
All proteins (and all rnas) must have the same length
Optional options:
--output -o output file where the results are saved. The format is "i j DCA APC"
Where for position "i" in the protein with position "j" of the RNA
the DCA and APC values are returned
--gaps -g (default: 0.5) Maximal percentage of gap [0, 1] in a column to be considered
--conservation -c (default 0.99) Maximal conservation [0, 1] in a column to be considered
--nbprocs -n (default 1) Number of processors to be used for the computation
The file Data/alignment.txt is the alignment used in "Unspecific binding but specific disruption of the group I intron by the StpA chaperone"
by Vladimir Reinharz & Tsvi Tlusty