Identify Coevolving Pairs
Refine MSA application.
-
evol_rankorder(mutinfo, **kwargs)[source]
Identify highly coevolving pairs of residues.
Parameters: | mutinfo – mutual information matrix |
Input Options
Parameters: |
- zscore (bool) – apply zscore for identifying top ranked coevolving pairs
- delimiter (str) – delimiter used in mutual information matrix file
- pdb (str) – PDB file that contains same number of residues as the mutual
information matrix, output residue numbers will be based on PDB
file
- msa (str) – MSA file used for building the mutual info matrix, output
residue numbers will be based on the most complete sequence in MSA
if a PDB file or sequence label is not specified
- label (str) – label in MSA file for output residue numbers
|
Output Options
Parameters: |
- numpairs (int) – number of top ranking residue pairs to list, default is
100
- seqsep (int) – report coevolution for residue pairs that are
sequentially separated by input value, default is 3
- dist (float) – report coevolution for residue pairs whose CA atoms are
spatially separated by at least the input value, used when a PDB
file is given and –use-dist is true, default is 10.0
- usedist (bool) – use structural separation to report coevolving pairs
- outname (str) – output filename, default is mutinfo_rankorder.txt
|