Specific K-mer Frequency

Evaluate frequency or usage deviation of a specific k-mer motif

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.

---

Source

proto-bio/proto-language/proto_language/constraint/sequence_composition/specific_kmer_constraint.py

View source

Evaluate frequency or usage deviation of a specific k-mer.

Supports two scoring modes:

1. Frequency mode: Raw k-mer frequency (count / total k-mer positions).
2. Usage deviation mode: Observed/expected ratio using a zero-order Markov model (product of individual character frequencies).

Metadata varies by mode:

Frequency mode:

• {kmer}_frequency: Float frequency value

Usage deviation mode:

• {kmer}_usage_deviation: Float observed/expected ratio
• {kmer}_count: Integer observed count
• {kmer}_expected: Float expected count

API Reference

ConfigSpecificKmerConfig Source

Configuration for evaluating a single specific k-mer.

For evaluating all k-mers of a given length, use KmerFrequencyConstraint.

kmer · string · required

The specific k-mer to evaluate (e.g., ‘CG’, ‘GATC’, ‘ATG’)

scoring_mode · enum · default: "frequency"

Scoring mode: ‘frequency’ for raw counts, ‘usage_deviation’ for observed/expected ratio

Options: frequency, usage_deviation

min_value · number · required

Minimum acceptable frequency/deviation based on scoring_mode

max_value · number · required

Maximum acceptable frequency/deviation based on scoring_mode

ReturnsConstraintOutput

One result per input sequence. The metadata field carries per-mode k-mer data (see Note).

Usage

python

from proto_language.core import Constraint
from proto_language.constraint import specific_kmer_constraint, SpecificKmerConfig

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

scores = constraint.evaluate()

Metadata

Property	Value
Key	specific-kmer-frequency
Function	specific_kmer_constraint
Category	sequence_composition
Mode	discrete
Uses GPU	False
Supported Types	dna, rna, protein