Reverse Complement of a DNA Sequence

This is a FREE and simple perl script which can be used to find the reverse complement of a DNA Sequence. This script generates the reverse complement of a DNA Sequence. This scripts runs both on windows and linux.

Perl Scripts for Bioinformatics to find the Reverse Complement of a DNA Sequence

Copy the below code and save it as " reverse-complement.pl " on your system.

# This script can be used to find the Reverse Complement in a DNA Sequence. # While executing this script it asks for the file name of the DNA sequence. # If the DNA sequence file is not in the same directory of this script, enter the file name with its full path. # Example: # In windows: c:\rnafile.txt # In Linux : /home/user/sequence/rnafile.txt # Send your comments and suggessions to techcuriosity @gmail.com # Website : http://www.techcuriosity.com use File::Path; print "\n\t#################### GET REVERSE COMPLEMENT OF DNA ####################\n\n"; print "PLEASE TYPE THE FILENAME OF THE DNA SEQUENCE := "; $dnafilename = <STDIN>; chomp $dnafilename; unless ( open(DNAFILE, $dnafilename) ) { print "Cannot open file \"$dnafilename\"\n\n"; exit; } @DNA = <DNAFILE>; close DNAFILE; $DNA = join( '', @DNA); $DNA =~ s/\s//g; print "\nTHE ORIGINAL DNA SEQUENCE :=\n$DNA\n\n"; @DNA = split( '', $DNA ); print"REVERSE COMPLEMENT OF THE DNA SEQUENCE :=\n"; foreach $nucleotide(reverse(@DNA)) { if ($nucleotide =~ /a/i) { print "T"; print WRITE "T"; } elsif ($nucleotide =~ /t/i) { print "A"; print WRITE "A"; } elsif ($nucleotide =~ /g/i) { print "C"; print WRITE "C"; } elsif ($nucleotide =~ /c/i) { print "G"; print WRITE "G"; } else { die "$0: Bad nucleotide! [$nucleotide]\n"; } }

Sample DNA Sequence - Save it as " dnafile.txt "

AATTCATTTTTAATCCTTTAATAGTCCACAGTAATATTGTCCTAAAGAGGGTACATTGG ATTTTAATTTTGCTTTCAATATGACGGCTGTCAATGTTGCCCTGATTCGTGATACCAAGTG GCTGACTTTAGAAGTCTGTAGAGAATTTCAGAGAGGAACTTGCTCTCGAGCTGATGCAGATT GCAAGTTTGCCCATCCACCAAGAGTTTGCCATGTGGAAAATGGTCGTGTGGTGGCCTGTTTTG ATTCTCTAAAGGGTCGGTGTACCCGAGAGAACTGCAAGTACCTTCACCCTCCTCCACACTTAA AAACGCAGCTGGAGATTAATGGGCGGAACAATCTGATTCAACAGAAGACTGCCGCAGCCATGTT CGCCCAGCAGATGCAGCTTATGCTCCAAAACGCTCAAATGTCATCACTTGGTTCTTTTCCTATG ACTCCATCAATTCCAGCTAATCCTCCCATGGCTTTCAATCCTTACATACCACATCCTGGGATGGG CCTCGTTCCTGCAGAACTTGTACCAAATACACCTGTTCTGATTCCTGGAAACCCACCTCTTGCAAT GCCAGGAGCTGTTGGCCCAAAACTGATGCGTTCAGATAAACTGGAGGTTTGCCGA

Result for reverse-complement.pl

>> perl reverse-complement.pl #################### GET REVERSE COMPLEMENT OF DNA #################### PLEASE TYPE THE FILENAME OF THE DNA SEQUENCE := ../bioseq/dnafile.txt THE ORIGINAL DNA SEQUENCE := AATTCATTTTTAATCCTTTAATAGTCCACAGTAATATTGTCCTAAAGAGGGTACATTGGATTTTAATTTTGCTTTCAATATGACGGCTGTCAATGTTGCCCTGATTCGTGATACCAAGTGGCTGACTTTAGAAGTCTGTAGAGAATTTCAGAGAGGAACTTGCTCTCGAGCTGATGCAGATTGCAAGTTTGCCCATCCACCAAGAGTTTGCCATGTGGAAAATGGTCGTGTGGTGGCCTGTTTTGATTCTCTAAAGGGTCGGTGTACCCGAGAGAACTGCAAGTACCTTCACCCTCCTCCACACTTAAAAACGCAGCTGGAGATTAATGGGCGGAACAATCTGATTCAACAGAAGACTGCCGCAGCCATGTTCGCCCAGCAGATGCAGCTTATGCTCCAAAACGCTCAAATGTCATCACTTGGTTCTTTTCCTATGACTCCATCAATTCCAGCTAATCCTCCCATGGCTTTCAATCCTTACATACCACATCCTGGGATGGGCCTCGTTCCTGCAGAACTTGTACCAAATACACCTGTTCTGATTCCTGGAAACCCACCTCTTGCAATGCCAGGAGCTGTTGGCCCAAAACTGATGCGTTCAGATAAACTGGAGGTTTGCCGA REVERSE COMPLEMENT OF THE DNA SEQUENCE := TCGGCAAACCTCCAGTTTATCTGAACGCATCAGTTTTGGGCCAACAGCTCCTGGCATTGCAAGAGGTGGGTTTCCAGGAATCAGAACAGGTGTATTTGGTACAAGTTCTGCAGGAACGAGGCCCATCCCAGGATGTGGTATGTAAGGATTGAAAGCCATGGGAGGATTAGCTGGAATTGATGGAGTCATAGGAAAAGAACCAAGTGATGACATTTGAGCGTTTTGGAGCATAAGCTGCATCTGCTGGGCGAACATGGCTGCGGCAGTCTTCTGTTGAATCAGATTGTTCCGCCCATTAATCTCCAGCTGCGTTTTTAAGTGTGGAGGAGGGTGAAGGTACTTGCAGTTCTCTCGGGTACACCGACCCTTTAGAGAATCAAAACAGGCCACCACACGACCATTTTCCACATGGCAAACTCTTGGTGGATGGGCAAACTTGCAATCTGCATCAGCTCGAGAGCAAGTTCCTCTCTGAAATTCTCTACAGACTTCTAAAGTCAGCCACTTGGTATCACGAATCAGGGCAACATTGACAGCCGTCATATTGAAAGCAAAATTAAAATCCAATGTACCCTCTTTAGGACAATATTACTGTGGACTATTAAAGGATTAAAAATGAA