ProfileHMM[PressedProtein]

A collection of profile Hidden Markov Models for amino acid sequences in binary format and indexed.

The hmmfile.h3m file contains the profile HMMs and their annotation in a binary format. The hmmfile.h3i file is an SSI index for the hmmfile.h3m file. The hmmfile.h3f file contains precomputed data structures for the fast heuristic filter (the MSV filter). The hmmfile.h3p file contains precomputed data structures for the rest of each profile.

Artifact Format

class ProfileHmmBinaryFileFmt(model.BinaryFileFormat):
    def _validate_(self, level):
        pass

class PressedProfileHmmsDirectoryFmt(model.DirectoryFormat):
    """
    The  <hmmfile>.h3m file contains the profile HMMs
    and their annotation in a binary format. The <hmmfile>.h3i file is an
    SSI index for the <hmmfile>.h3m file.  The <hmmfile>.h3f file contains
    precomputed data structures for the fast heuristic filter
    (the MSV filter).  The <hmmfile>.h3p file contains precomputed data
    structures for the rest of each profile.
    """
    h3m = model.File(r'.*\.hmm\.h3m', format=ProfileHmmBinaryFileFmt)
    h3i = model.File(r'.*\.hmm\.h3i', format=ProfileHmmBinaryFileFmt)
    h3f = model.File(r'.*\.hmm\.h3f', format=ProfileHmmBinaryFileFmt)
    h3p = model.File(r'.*\.hmm\.h3p', format=ProfileHmmBinaryFileFmt)

Expected Folder Structure

data
├── <taxon_id>.hmm.h3m
├── <taxon_id>.hmm.h3i
├── <taxon_id>.hmm.h3f
└── <taxon_id>.hmm.h3p

Where to find ProfileHMM[PressedProtein]

• The Functional Annotation of MAGs (or Contigs) tutorial.

Actions that use ProfileHMM[PressedProtein] artifacts:

As Output

• fetch‐eggnog‐hmmer‐db

As Input

• eggnog-hmmer-search