> ## Documentation Index > Fetch the complete documentation index at: https://proto.evodesign.org/docs/llms.txt > Use this file to discover all available pages before exploring further. # Protein Repetitiveness > Evaluate protein sequence repetitiveness based on k-mer analysis

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

evo-design/proto-language/proto\_language/constraint/protein\_quality/protein\_repetitiveness\_constraint.py

View source

Constraint contributors

Evaluate protein sequence repetitiveness based on k-mer frequency analysis. This constraint function analyzes protein sequences for repetitive content by examining k-mer frequencies. It identifies sequences with excessive repetitive motifs, which may indicate low-complexity regions or non-functional proteins. The analysis scans multiple k-mer lengths to detect both short tandem repeats and larger sequence duplications. The repetitiveness score represents the maximum fraction of the sequence covered by any repeated k-mer. For example, if "SSS" appears 8 times in a 60-amino-acid sequence, the repetitiveness for 3-mers is (8 \* 3) / 60 = 0.4 (40% of sequence). ## API Reference

ConfigProteinRepetitivenessConfig Source

Configuration for protein repetitiveness constraint. This class defines configuration parameters for evaluating repetitive content in protein sequences using k-mer frequency analysis. The constraint detects and penalizes sequences with excessive tandem repeats or repetitive motifs, which may indicate low-complexity regions or non-functional proteins. The repetitiveness score is calculated as the maximum fraction of the sequence covered by any repeated k-mer. For example, if "AAA" appears 10 times in a 100-amino-acid sequence, the repetitiveness for 3-mers is (10 \* 3) / 100 = 0.3 (30% of sequence). Maximum acceptable repetitiveness fraction (fraction of sequence covered by repeated k-mers) Smallest k-mer length treated as a repeat; the scan continues up to this length plus 6.

ReturnsConstraintOutput

One result per sequence. A score of 0.0 indicates acceptable repetitiveness (at or below threshold) and higher values indicate excessive repetitive content. Penalties scale linearly with excess repetitiveness: if max is 0.4 and actual is 0.6, the excess (0.2) is normalized by the remaining range (1.0 - 0.4 = 0.6), giving a score of 0.33. `metadata` carries: * `repetitiveness_score`: Float repetitiveness score (0.0-1.0) representing the maximum fraction of sequence covered by repeated k-mers * `max_repetitive_fraction`: Float identical to `repetitiveness_score`

## Usage Evaluating repetitiveness with default settings: ```python python icon="python" theme={null} >>> from proto_language.core import Sequence, SequenceType >>> config = ProteinRepetitivenessConfig(max_repetitiveness=0.4, min_repeat_length=3) >>> seq = Sequence("MVLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSF", "protein") >>> results = protein_repetitiveness_constraint([(seq,)], config) >>> print(results[0].score) # 0.0 if repetitiveness < 40% >>> print(results[0].metadata["repetitiveness_score"]) # e.g., 0.15 ``` ## Metadata | Property | Value | | --------------- | ----------------------------------- | | Key | `protein-repetitiveness` | | Function | `protein_repetitiveness_constraint` | | Category | `protein_quality` | | Mode | `discrete` | | Uses GPU | `False` | | Supported Types | `protein` |