> ## 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 Complexity > Evaluate protein sequence complexity using segmasker to detect low-complexity regions

**License:** Segmasker is licensed under Custom (NCBI BLAST+ public domain). Please refer to [the license](https://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/lxr/source/scripts/projects/blast/LICENSE) for full terms.

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

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```bibtex theme={null} @article{wootton1993seg, title={Statistics of local complexity in amino acid sequences and sequence databases}, author={Wootton, John C and Federhen, Scott}, journal={Computers \& Chemistry}, volume={17}, number={2}, pages={149--163}, year={1993}, publisher={Elsevier}, doi={10.1016/0097-8485(93)85006-x} } @article{camacho2009blastplus, title={BLAST+: architecture and applications}, author={Camacho, Christiam and Coulouris, George and Avagyan, Vahram and Ma, Ning and Papadopoulos, Jason and Bealer, Kevin and Madden, Thomas L}, journal={BMC Bioinformatics}, volume={10}, pages={421}, year={2009}, publisher={BioMed Central}, doi={10.1186/1471-2105-10-421} } ```

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Evaluate protein sequence complexity using segmasker to detect low-complexity regions. This constraint function uses NCBI's segmasker tool to identify low-complexity regions in protein sequences. Low-complexity regions contain repetitive or compositionally biased amino acid sequences that may indicate poor protein quality, tandem repeats, or non-functional segments. The constraint penalizes sequences where the fraction of low-complexity regions exceeds a specified threshold. The function processes multiple sequences simultaneously. Segmasker marks low-complexity regions by replacing them with lowercase characters, and the constraint calculates the fraction of masked positions. ## API Reference

ConfigProteinComplexityConfig Source

Configuration for protein complexity constraint. This class defines configuration parameters for evaluating protein sequence complexity using NCBI's segmasker tool. The constraint detects and penalizes low-complexity regions, which contain repetitive or biased amino acid compositions that may indicate poor protein quality or non-functional sequences. Maximum acceptable fraction of low-complexity regions (repetitive/biased amino acid compositions)

ReturnsConstraintOutput

One result per sequence. A score of 0.0 indicates acceptable complexity (low-complexity fraction at or below threshold) and higher values indicate excessive low-complexity content. Scores scale linearly with excess low-complexity beyond the threshold, capped at 1.0. `metadata` carries: * `low_complexity_fraction`: Float fraction of sequence identified as low-complexity (0.0-1.0) * `low_complexity_count`: Integer count of positions masked as low-complexity (from segmasker)

## Usage Evaluating protein complexity: ```python python icon="python" theme={null} >>> from proto_language.core import Sequence, SequenceType >>> config = ProteinComplexityConfig(max_low_complexity=0.2) >>> seq = Sequence("MVLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSF", "protein") >>> results = protein_complexity_constraint([(seq,)], config) >>> print(results[0].score) # 0.0 if low-complexity <= 20% >>> print(results[0].metadata["low_complexity_fraction"]) # e.g., 0.15 >>> print(results[0].metadata["low_complexity_count"]) # e.g., 5 ``` ## Metadata | Property | Value | | --------------- | ------------------------------- | | Key | `protein-complexity` | | Function | `protein_complexity_constraint` | | Category | `protein_quality` | | Mode | `discrete` | | Uses GPU | `False` | | Supported Types | `protein` |