How to Reverse Complement of DNA Sequence in Bash

Renesh Bedre    1 minute read

The reverse complement of a DNA sequence is obtained by reversing the DNA sequence and replacing each nucleotide with its complementary base. For example, the reverse complement of the “AATGTACTAT” sequence is “ATAGTACATT”.

The following examples demonstrate how to get reverse complement of DNA sequence using BASH commands:

Example 1

The tr (translate) and rev (reverse) commands can be used for getting the reverse complement of DNA sequence.

# example sequence AATGTACTAT
echo "AATGTACTAT" | tr 'ATCGatcg' 'TAGCtagc' | rev



Example 2

The following awk command can be used for getting the reverse complement of all DNA sequences from the FASTA file.

For example, the input.fasta file contains the following two sequences,

# input.fasta

Now, perform the reverse complement of DNA sequences from the FASTA file using awk,

awk '/^>/ { if (seq) system("echo "seq"| tr 'ATCGatcg' 'TAGCtagc' | rev"); printf "%s\n", $0; seq=""; next } { seq = seq $0 } END { if (seq) system("echo "seq"| tr 'ATCGatcg' 'TAGCtagc' | rev")} ' input.fa



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