Transcription and Translation - Usage Guide

Overview

This skill enables AI agents to help you convert between DNA, RNA, and protein sequences using Biopython. It covers transcription, back-transcription, and translation, with emphasis on the decisions that silently corrupt results: choosing the correct NCBI genetic code, validating coding sequences, and handling partial codons, gaps, and recoded stops.

Prerequisites

pip install biopython

Quick Start

Tell your AI agent what you want to do:

• "Transcribe this DNA sequence to RNA"
• "Translate this coding sequence to protein"
• "Translate this human mitochondrial gene with the right genetic code"
• "Validate that this is a complete CDS and translate it"
• "Find all open reading frames longer than 100 amino acids"
• "Show me the translation in all six reading frames"

Example Prompts

Basic Transcription

"Convert this DNA to RNA: ATGCGATCGATCG"

Template-Strand Transcription

"This is the template strand, give me the mRNA it produces"

Basic Translation

"Translate this DNA sequence to protein"

Stop Codon Handling

"Translate this sequence but stop at the first stop codon"

Alternative Genetic Codes

"This is from E. coli, translate it with the bacterial code"

Mitochondrial Sequences

"Translate this human mitochondrial sequence with the correct table"

CDS Validation

"Check that this is a valid complete CDS, then translate it"

ORF Finding

"Find all open reading frames longer than 100 amino acids"

Six-Frame Translation

"Show me the translation in all six reading frames"

What the Agent Will Do

1. Confirm the molecule type and strand (no type checks exist since Biopython 1.78)
2. Create a Seq object from your sequence
3. Select the correct NCBI codon table for the organism if it is not standard
4. Apply transcribe, back_transcribe, or translate with the right options
5. Use cds=True to validate complete coding sequences and surface defects loudly
6. Return the converted sequence(s)

Codon Tables

Biopython includes every NCBI genetic code. The choice changes the protein, and a valid-but-wrong table produces a plausible wrong result with no error:

• 1 (Standard): Most nuclear genes
• 2 (Vertebrate Mitochondrial): Human/vertebrate mtDNA; AGA/AGG are stops, AUA=Met, UGA=Trp
• 3 (Yeast Mitochondrial): CTG=Thr lives here (not table 12)
• 4 (Mold/Protozoan Mito + Mycoplasma): UGA=Trp
• 5 (Invertebrate Mitochondrial): AGA/AGG=Ser
• 6 (Ciliate Nuclear): UAA/UAG=Gln
• 11 (Bacterial/Archaeal/Plastid): expanded start codons
• 12 (Alternative Yeast Nuclear): CUG=Ser (not Thr)

Tips

• Translation works directly on both DNA and RNA, so explicit transcription is rarely needed first.
• A wrong codon table is the most common silent bug; pick the organism's table deliberately.
• Use cds=True for complete coding sequences; it raises on a bad start, length, or stop instead of returning a wrong protein silently.
• An alternative start (GTG/TTG/ATT) under cds=True is translated as M, which is biologically correct.
• A length not divisible by 3 only warns and drops trailing bases; cds=True turns that into a loud error.
• transcribe() and back_transcribe() only swap T and U; they do not splice, cap, or add poly-A. For real transcription from the template strand, reverse-complement first.
• Selenocysteine (UGA) and pyrrolysine (UAG) are not recoded by Biopython; they appear as * or silently truncate with to_stop=True.

Related Skills

• seq-objects - Create and inspect Seq objects before translation
• reverse-complement - Strand handling for six-frame translation and template-strand transcription
• codon-usage - Analyze codon bias and adaptation in coding sequences
• sequence-io/read-sequences - Parse GenBank/FASTA records and CDS features for translation