MSA Refinement

Refine MSA application.

prody.apps.evol_apps.evol_refine.evol_refine(msa, **kwargs)[source]

Refine an MSA by removing gapped rows/colums.

Parameters:

msa – MSA filename to be refined

Refinement Options

Parameters:

  • label (str) – sequence label, UniProt ID code, or PDB and chain identifier

  • seqid (float) – identity threshold for selecting unique sequences

  • colocc (float) – column (residue position) occupancy

  • rowocc (float) – row (sequence) occupancy

  • pdbres (bool) – keep columns corresponding to residues not resolved in PDB structure, applies label argument is a PDB identifier

Output Options

Parameters:

  • outname (str) – output filename, default is msa filename with _refined suffix

  • format (str) – output MSA file format, default is same as input

  • compressed (bool) – gzip refined MSA output