Biology Foundations

Overview

Sequence primitives in quantsmind.biology (sequences.py): DNA/RNA validation, complement, transcription, standard-code translation, and GC statistics.

Purpose

Let users run the central dogma (DNA → RNA → protein) on real sequence fragments with nothing to install beyond the SDK.

Concept

Sequences are validated uppercase strings; translation walks codons via the 64-entry CODON_TABLE, stopping before the first stop codon and ignoring a trailing partial codon.

API

validate_dna(), validate_rna(), complement(), reverse_complement(), transcribe(), translate_rna(), translate_dna(), gc_content(), hamming_distance(), point_mutation(), CODON_TABLE, alphabets.

Input / Processing / Output

Input: base strings. Processing: validation + mapping. Output: strings and the GC fraction in [0, 1].

Example

python examples/biology/central_dogma.py transcribes and translates a 24-base fragment into MAIVMGR.

Limitations

Educational scope only: no alignment, no phylogeny, no clinical or diagnostic use, no production bioinformatics.