GC Content

Enforce GC content within specified range

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Source

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

View source

Enforce GC content within specified range.

This constraint function calculates the percentage of guanine (G) and cytosine (C) nucleotides in DNA or RNA sequences and evaluates whether it falls within a specified acceptable range. GC content is a fundamental sequence property that affects DNA stability, melting temperature, gene expression patterns, and technical considerations like PCR amplification efficiency.

API Reference

ConfigGCContentConfig Source

Configuration for GC content constraint.

This class defines configuration parameters for evaluating the GC content in DNA or RNA sequences. This penalty scales linearly with deviation from the acceptable range.

min_gc · number · required

Minimum acceptable GC content percentage (0-100)

max_gc · number · required

Maximum acceptable GC content percentage (0-100)

ReturnsConstraintOutput

One result per sequence. A score of 0.0 indicates GC content is within the acceptable range [min_gc, max_gc]. Higher scores indicate greater deviation from the acceptable range, with penalties scaling linearly with the deviation distance. The metadata field carries gc_content.

Usage

Evaluating GC content constraint:

python

>>> seq = Sequence("ATCGATCG", "dna")
>>> cfg = GCContentConfig(min_gc=40.0, max_gc=60.0)
>>> result = gc_content_constraint([(seq,)], config=cfg)
>>> print(result[0].score)  # 0.0 (50% GC content is within acceptable range)

Metadata

Property	Value
Key	gc-content
Function	gc_content_constraint
Category	sequence_composition
Mode	discrete
Uses GPU	False
Supported Types	dna, rna