Protein Profile HMM

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.

API Reference

ConfigProteinProfileHMMConfig Source

Configuration for profile-HMM matching.

string

required

Path to a profile-HMM file for hmmsearch.

List[string]

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

boolean

default:"True"

Require all listed profiles instead of any listed profile.

enum

default:"query_name"

HMM hit field used to match required profile strings.Options: query_name, query_accession, query_description

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()

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

Property

Value

Key

protein-profile-hmm

Function

protein_profile_hmm_constraint

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Protein Profile HMM

API Reference

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API Reference

Usage

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