Evol Application

Evol applications have similar fuctionality as the python API. We can search Pfam, fetch from Pfam and also refine MSA, merge two or more MSA and calculate conservation and coevolution properties and also rankorder results from mutual information to get top-ranking pairs.

All 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.sth -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.sth -S
evol coevol PF00074_full_refined.sth -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 a PDB file, such as the one we made earlier:

evol rankorder -h
evol rankorder PF00074_full_refined_mutinfo_corr_apc.txt -q 5 -p 2W5IB_3-121.pdb
evol rankorder PF00074_full_refined_mutinfo_corr_apc.txt -u -t 15 -p 2W5IB_3-121.pdb

We can also provide a PDB ID and chain if we provide an MSA to match it against:

evol rankorder PF00074_full_refined_mutinfo_corr_apc.txt -q 5 -p 2W5IB -m PF00074_full_refined.sth

Or even use the MSA directly if it has start and end in the labels:

evol rankorder PF00074_full_refined_mutinfo_corr_apc.txt -q 5 -m PF00074_full_refined.sth -l RNAS1_BOVIN