Evol Applications have similar fuctionality as the python API. We can
fetch from Pfam and also
merge two or more MSA
coevolution properties and also
rankorder results from mutual information to get top-ranking pairs.
evol functions and their options can be obtained using the -h option.
We should be in /prody/scripts directory to run the following commands:
evol -h evol search -h evol search 2W5IB evol fetch PF00074
Using the above we can search and fetch MSA. Next we can refine the MSA:
evol refine -h evol refine PF00074_full.slx -l RNAS1_BOVIN -s 0.98 -r 0.8
Next we can calculate conservation using shannon entropy and coevolution using mutual information with correction and also save the plots.:
evol conserv PF00074_full_refined.slx -S evol coevol PF00074_full_refined.slx -S -F png -c apc -cmin 0.0
We can rank order the residues with highest covariance and apply filters like reporting only those pairs that are at a separation of at least 5 residues sequentially or are 15 Ang apart in structure. The residues may be numbered based on PDB:
evol rankorder -h evol rankorder PF00074_full_refined_mutinfo_corr_apc.txt -q 5 -p 2W5IBI_1-121.pdb evol rankorder PF00074_full_refined_mutinfo_corr_apc.txt -u -t 15 -p 2W5IB_1-121.pdb