Protein Profile HMM

Search proteins, or longest ORFs from DNA, against a profile-HMM file.

License: This constraint can use multiple tools, each under its own license. See the Tools Used tab and each tool’s page for license details.

This constraint is open source. Any third-party models, product names, or trademarks referenced are the property of their respective owners, and Proto is not affiliated with them.

---

Tools Used Tools Used Source Source

proto-bio/proto-language/proto_language/constraint/protein_quality/protein_profile_hmm_constraint.py

View source

Require profile-HMM support for proteins or translated DNA sequences.

API Reference

ConfigProteinProfileHMMConfig Source

Configuration for profile-HMM matching.

hmm_path · string · required

Path to a profile-HMM file for hmmsearch.

required_profiles · List[string]

Profile names/accessions/descriptions that must be detected. Empty means any HMM hit passes.

match_all_required_profiles · boolean · default: "True"

Require all listed profiles instead of any listed profile.

profile_match_field · enum · default: "query_name"

HMM hit field used to match required profile strings.

Options: query_name, query_accession, query_description

hmmsearch_config · PyHmmsearchConfig

PyHMMER hmmsearch configuration. Tune evalue_threshold / domain_evalue_threshold here.

ReturnsConstraintOutput

One output per proposal. A score of 0.0 passes and 1.0 fails. Metadata contains selected ORF details for DNA, sequence/domain HMM hits, and matched required profiles.

Usage

python

from proto_language.core import Constraint
from proto_language.constraint import protein_profile_hmm_constraint, ProteinProfileHMMConfig

constraint = Constraint(
    inputs=[segment],
    function=protein_profile_hmm_constraint,
    function_config=ProteinProfileHMMConfig(
        # Configure parameters here
    ),
)

scores = constraint.evaluate()

Metadata

Property	Value
Key	protein-profile-hmm
Function	protein_profile_hmm_constraint
Category	protein_quality
Mode	discrete
Uses GPU	False
Supported Types	dna, protein