Reverse Complement - Usage Guide

Overview

This skill enables AI agents to help you generate complementary and reverse complementary sequences using Biopython. It covers the everyday operation (opposite strand, 5'->3'), the RNA-specific methods, IUPAC ambiguity codes, gapped alignment columns, in-place mutation, and the silent-corruption traps (protein sequences, double reverse-complementing minus-strand features, confusing complement with transcription).

Prerequisites

pip install biopython

Quick Start

Tell your AI agent what you want to do:

• "Get the reverse complement of this sequence"
• "Show me both strands of this DNA"
• "Is this a palindromic sequence?"
• "Design a reverse primer for this region"
• "Get the coding sequence for this minus-strand gene"
• "Reverse complement every sequence in this FASTA file"

Example Prompts

Basic Reverse Complement

"What is the reverse complement of ATGCGATCGATCG?"

Visualize Double-Stranded DNA

"Show me this sequence as double-stranded DNA with both strands"

Palindrome Check

"Is GAATTC a palindromic sequence? What about ATGCAT?"

RNA Strand

"Give me the reverse complement of this RNA but keep it as U, not T"

Primer Design

"I need to amplify positions 100-500 of this sequence. What would the reverse primer look like?"

Minus-Strand Feature

"This CDS is annotated on the minus strand. Extract its coding sequence in the right orientation."

Strand Conversion

"Convert this template strand sequence to the coding strand"

What the Agent Will Do

1. Wrap your input in a Bio.Seq.Seq object (or read records with SeqIO)
2. Confirm the molecule type so it does not silently reverse-complement a protein
3. Pick the method: reverse_complement() for DNA, reverse_complement_rna() to keep U, complement() for same-direction base pairs
4. For an annotated feature, use feature.extract() which already handles minus-strand orientation
5. Return the result in the conventional 5'->3' orientation

Understanding the Methods

• reverse_complement(): What you usually want. Gives the opposite strand in 5'->3' direction. Runs in DNA mode, so any U is treated as T and emitted as T.
• reverse_complement_rna() / complement_rna(): Use these to keep RNA output (U, not T).
• complement(): Less common. Gives base pairs without reversing (3'->5' of the opposite strand).
• transcribe(): NOT a complement. It only swaps T->U on the same strand. To transcribe from a template strand: template.reverse_complement().transcribe().

Strand Terminology

Coding strand:     5'-ATGCGATCG-3'  (matches mRNA, except T instead of U)
Template strand:   3'-TACGCTAGC-5'  (used for transcription)
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reverse_complement() of the coding strand = the template strand (written 5'->3').

Tips

• For primer design, the reverse primer is the reverse complement of your target region's 3' end.
• Restriction enzyme sites are often palindromic - they equal their own reverse complement (S, W, and N bases are themselves self-complementary).
• When searching for motifs, search both the sequence and its reverse complement.
• Biopython handles all 15 IUPAC ambiguity codes correctly and case-insensitively. Never hand-roll the complement table - B/V and D/H are easy to swap and the error is silent.
• complement() and reverse_complement() do NOT validate the alphabet. Gaps (-) pass through unchanged (good for aligned sequences), but a protein passed in by mistake produces silent garbage with no warning - guard on molecule_type.
• After feature.extract() on a minus-strand feature, do NOT reverse-complement again; extract() already did it.
• inplace=True only works on a MutableSeq; on an immutable Seq it raises TypeError.

Related Skills

• seq-objects - Create and mutate Seq/MutableSeq objects to complement
• transcription-translation - transcribe() vs complement(); six-frame translation uses the reverse complement
• motif-search - Search both strands by reverse-complementing the query or sequence
• sequence-io/read-sequences - Parse FASTA/GenBank records before reverse-complementing
• primer-design/primer-basics - Reverse primers are the reverse complement of the target 3' end
• restriction-analysis/restriction-sites - Restriction sites are often palindromic (self-complementary)