DNA Reverse Complement

About DNA Reverse Complement

This tool takes a DNA or RNA sequence and gives back its reverse complement, its plain complement, or just the reversed string. It understands IUPAC ambiguity codes, so a degenerate primer such as one containing R or Y complements correctly instead of being mangled. It is the quickest way to turn a forward-strand sequence into the opposite strand read 5' to 3'.

How to use it

1. Paste the sequence into the Sequence box. The line under it reports how many valid bases were recognized.
2. Open the Transform menu and pick Reverse complement, Complement, or Reverse.
3. Tick the RNA (use U) checkbox if you want uracil in the output instead of thymine.
4. Read the result in the Result panel, then use Copy sequence for the bare string or Copy FASTA for a wrapped record with a header.

Reverse complement with ambiguity codes

GAATTCRYN

NRYGAATTC

When to use it

• Turning the forward-strand sequence at the end of a gene into the reverse primer you will order.
• Checking that a restriction site is palindromic, meaning it equals its own reverse complement.
• Reading a feature annotated on the minus strand of a genome browser record as it would appear in the mRNA.
• Comparing a read that came off a sequencer in the opposite orientation against a reference.

Questions about DNA Reverse Complement

Why is the reverse complement different from the complement?

The two strands of a double helix run antiparallel. Complementing alone keeps the left-to-right order, which reads 3' to 5'. Reversing as well gives the opposite strand in the conventional 5' to 3' direction.

How are degenerate bases handled?

Each ambiguity code maps to the code covering the complementary bases: R and Y swap, K and M swap, B and V swap, D and H swap, while S, W and N stay the same. A gap dash is also carried through unchanged.

What happens to spaces, digits and line breaks in my paste?

Anything that is not a valid nucleotide letter is dropped, so numbered GenBank-style text works. A FASTA header line that starts with a greater-than sign is skipped, and if several records are pasted only the first is used.

Does the RNA checkbox change how I should enter the input?

No. Input is normalized first, so U and T are both accepted. The checkbox only decides whether the output is written with U or T.

Is there a length limit?

Input is capped at 100,000 valid bases, which is far more than any primer or typical gene needs.

Related tools

• Sequence ManipulatorExtract a subsequence, soft/hard-mask a region, reverse, complement, or change the case of any DNA, RNA, or protein sequence.
• DNA to RNA TranscriptionTranscribe a DNA coding or template strand into mRNA, or reverse-transcribe RNA back to DNA.
• FASTA FormatterParse, clean, validate, and re-wrap FASTA records at a chosen line width.
• Six-Frame TranslationTranslate a DNA or RNA sequence in all six reading frames (three forward, three reverse) to find coding potential.
• DNA to Protein TranslationTranslate a DNA or RNA sequence into protein across reading frames using the standard genetic code.
• ORF FinderFind open reading frames (ATG to stop) across all six frames, with position, length, and protein.