Bio Reverse Complement

Version Compatibility

Reference examples tested with: BioPython 1.83+

Before using code patterns, verify installed versions match. If versions differ:

• Python: pip show <package> then help(module.function) to check signatures

If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying.

Reverse Complement

Generate complementary and reverse complementary sequences using Biopython.

"Get the reverse complement" -> Produce the 5'-to-3' sequence of the opposite strand.

• Python: seq.reverse_complement() (BioPython Seq)
• CLI: samtools faidx ref.fa region --reverse-complement (extracts and RCs a region)

The Governing Principle

Never hand-roll the complement table. Biopython's reverse_complement() already encodes the full IUPAC mapping correctly, case-insensitively, and on minus-strand features it is applied for the analyst automatically by SeqFeature.extract(). Every silent corruption in this domain comes from reimplementing what Biopython already does right: swapping ambiguity codes, forgetting that S/W/N are self-complementary, complementing the wrong molecule type, or reverse-complementing a second time after extract() already did it. Reach for the library method; reach for a guard (molecule_type) before it; never reach for a custom dictionary.

Required Import

from Bio.Seq import Seq

Which Method for Which Question

reverse_complement()

Returns the reverse complement (5'->3' of the opposite strand). This is the most commonly used operation.

seq = Seq('ATGCGATCG')
rc = seq.reverse_complement()  # Returns Seq('CGATCGCAT')

complement()

Returns the complement without reversing. Less common - gives the opposite strand still written in 3'->5' order.

seq = Seq('ATGCGATCG')
comp = seq.complement()  # Returns Seq('TACGCTAGC')

reverse_complement_rna() and complement_rna()

For RNA, the dedicated methods emit U:

rna = Seq('AUGCGAUCG')
rna.reverse_complement_rna()  # Returns Seq('CGAUCGCAU')
rna.complement_rna()          # Returns Seq('UACGCUAGC')

Base Pairing and Ambiguity Codes

reverse_complement() complements all 15 IUPAC codes plus X correctly. The mapping is non-obvious for ambiguity codes - this is exactly why hand-rolling corrupts silently.

S, W, N, and X are SELF-complementary. The pairs that get swapped wrong by hand are B<->V and D<->H. The table is built for upper and lower case, so complementation is case-insensitive (Seq('atRY').reverse_complement() works).

DNA vs RNA: the U handling rule

reverse_complement() runs in DNA mode: it treats any U as a T and EMITS T (docstring: "Any U in the sequence is treated as a T"). It does not raise and does not leave U.

Seq('ACGU').reverse_complement()      # Returns Seq('ACGT')  -- U mapped to A, emitted as T
Seq('ACGU').reverse_complement_rna()  # Returns Seq('ACGU')  -- stays RNA

transcribe() does NOT complement. It swaps T->U on the SAME strand. Confusing "complement the template" with "transcribe the coding strand" is silent corruption. True biological transcription from the template strand is template_dna.reverse_complement().transcribe().

Gaps and Non-Table Characters

complement and reverse_complement do NOT validate the alphabet (unlike translate()). A gap - is not a table key, so it passes through unchanged and reversal preserves gap columns - the desired behavior for aligned sequences. Any other non-table character (?, *) also passes through silently.

Seq('ATG-CGA--TY').reverse_complement()  # Returns Seq('RA--TCG-CAT') -- gaps preserved, Y->R

Because there is no alphabet check, garbage in produces garbage out without a warning (see the protein trap below).

Code Patterns

Visualize Double-Stranded DNA

def show_dsdna(seq):
    print(f"5'-{seq}-3'")
    print(f"   {'|' * len(seq)}")
    print(f"3'-{seq.complement()}-5'")

show_dsdna(Seq('ATGCGATCG'))

Check if a Sequence is Palindromic (Self-Complementary)

def is_palindrome(seq):
    return seq == seq.reverse_complement()

is_palindrome(Seq('GAATTC'))  # True  -- EcoRI site
is_palindrome(Seq('ATGCGA'))  # False

Reverse Complement a FASTA File

Goal: Produce a new FASTA file with all sequences reverse-complemented.

Approach: Parse records as a stream, build new SeqRecords from .reverse_complement(), write to output.

Reference (BioPython 1.83+):

from Bio import SeqIO
from Bio.SeqRecord import SeqRecord

def reverse_complement_records(records):
    for record in records:
        yield SeqRecord(record.seq.reverse_complement(), id=record.id + '_rc', description=record.description + ' reverse complement')

records = SeqIO.parse('sequences.fasta', 'fasta')
SeqIO.write(reverse_complement_records(records), 'sequences_rc.fasta', 'fasta')