Transcription and Translation - Usage Guide

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 the central dogma operations: transcription, back-transcription, and translation with support for alternative codon tables.

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"
• "Find all open reading frames in this sequence"
• "Translate using the mitochondrial codon table"

Example Prompts

Basic Transcription

"Convert this DNA to RNA: ATGCGATCGATCG"

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 using the bacterial codon table"

Mitochondrial Sequences

"Translate this human mitochondrial sequence"

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. Import Bio.Seq
2. Create a Seq object from your sequence
3. Apply the appropriate method (transcribe, translate, etc.)
4. Handle codon table selection if needed
5. Return the converted sequence(s)

Codon Tables

Biopython includes all NCBI codon tables. Common ones:

• 1 (Standard): Most nuclear genes
• 2 (Vertebrate Mitochondrial): Human, mouse, etc. mitochondria
• 11 (Bacterial): E. coli, plastids, most prokaryotes
• 4 (Mold Mitochondrial): Fungi, some protists
• 5 (Invertebrate Mitochondrial): Insects, worms

Tips

• Translation works on both DNA and RNA sequences
• Use to_stop=True to get clean protein without the * character
• Use cds=True for validated coding sequences (will error if invalid)
• For finding ORFs, search all six reading frames
• Mention the organism if using non-standard codon tables