Mutation - DNA Sequence

This is a FREE and simple perl script which can be used to mutate a DNA Sequence. This script randomly generates 10 successive mutation result. This scripts runs both on windows and linux.

Perl Scripts for Bioinformatics to mutate a DNA Sequence

Copy the below code and save it as "mutation.pl" on your system.

# This script can be used to Mutate a DNA Sequence. # This script randomly mutates the DNA sequence and generates 10 successive mutation results. # 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 suggestions to techcuriosity @gmail.com # Website : http://www.techcuriosity.com use File::Path; print "\n\t#################### MUTATION OF DNA ####################\n\n"; print "ENTER THE FILENAME OF THE DNA SEQUENCE:= "; $dnafilename = <STDIN>; chomp $dnafilename; unless ( open(DNAFILE, $dnafilename) ) { print "Cannot open file \"$dnafilename\"\n\n"; goto h; } my $DNA = <DNAFILE>; close DNAFILE; my $i; my $mutant; $mutant = mutate($DNA); print "Mutate DNA\n\n"; print "HERE IS THE ORIGINAL DNA SEQUENCE:\n"; print "$DNA\n\n"; print "HERE IS THE MUTANT DNA SEQUENCE:\n"; print "$mutant\n\n"; print "HERE ARE THE 10 SUCCESSIVE MUTATIONS:\n\n"; for ($i=0 ; $i < 10 ; ++$i) { $mutant = mutate($mutant); print "$mutant\n"; print WRITE "$mutant\n"; } sub mutate { my($dna) = @_; my($position) = randomposition($dna); my $current_base = substr($dna, $position, 1); my $newbase; do { $newbase = randomnucleotide(); } until ($newbase ne $current_base); substr($dna,$position,1,$newbase); return $dna; } sub randomposition { my($string) = @_; return int rand length $string; } sub randomelement { my(@array) = @_; return $array[rand @array]; } sub randomnucleotide { my(@nucleotides) = ('A', 'C', 'G', 'T'); return randomelement(@nucleotides); }

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

AATTCATTTTTAATCCTTTAATAGTCCACAGTAATATTGTCCTAAAGAGGGTACATTGG ATTTTAATTTTGCTTTCAATATGACGGCTGTCAATGTTGCCCTGATTCGTGATACCAAGTG GCTGACTTTAGAAGTCTGTAGAGAATTTCAGAGAGGAACTTGCTCTCGAGCTGATGCAGATT GCAAGTTTGCCCATCCACCAAGAGTTTGCCATGTGGAAAATGGTCGTGTGGTGGCCTGTTTTG ATTCTCTAAAGGGTCGGTGTACCCGAGAGAACTGCAAGTACCTTCACCCTCCTCCACACTTAA AAACGCAGCTGGAGATTAATGGGCGGAACAATCTGATTCAACAGAAGACTGCCGCAGCCATGTT CGCCCAGCAGATGCAGCTTATGCTCCAAAACGCTCAAATGTCATCACTTGGTTCTTTTCCTATG ACTCCATCAATTCCAGCTAATCCTCCCATGGCTTTCAATCCTTACATACCACATCCTGGGATGGG CCTCGTTCCTGCAGAACTTGTACCAAATACACCTGTTCTGATTCCTGGAAACCCACCTCTTGCAAT GCCAGGAGCTGTTGGCCCAAAACTGATGCGTTCAGATAAACTGGAGGTTTGCCGA

Result for mutation.pl

>> perl mutation.pl #################### MUTATION OF DNA #################### ENTER THE FILENAME OF THE DNA SEQUENCE:= ../bioseq/dnafile.txt Mutate DNA HERE IS THE ORIGINAL DNA SEQUENCE: AATTCATTTTTAATCCTTTAATAGTCCACAGTAATATTGTCCTAAAGAGGGTACATTGGATTTTAATTTTGCTTTCAATATGACGGCTGTCAATGTTGCCCTGATTCGTGATACCAAGTG HERE IS THE MUTANT DNA SEQUENCE: AATTCATTCTTAATCCTTTAATAGTCCACAGTAATATTGTCCTAAAGAGGGTACATTGGATTTTAATTTTGCTTTCAATATGACGGCTGTCAATGTTGCCCTGATTCGTGATACCAAGTG HERE ARE THE 10 SUCCESSIVE MUTATIONS: AATTCATTCTTAATCCTTTAATAGTCCACAGTAATATTGTCCTAAAGAGGGTACATTGGATTTTAATTTTGCTTTCAATATGACGGCTGTCAATGTTGCCCTGATTCGGGATACCAAGTG AATTCATTCTTAATCCTTTAATAGTCCACAGTAATATTGTCCTAAAGAGGGTACATTGGATTTTAATTTTGCTTTCAATATGACGGCTGTCAATGTTGCCCTGATTCGAGATACCAAGTG AATTCTTTCTTAATCCTTTAATAGTCCACAGTAATATTGTCCTAAAGAGGGTACATTGGATTTTAATTTTGCTTTCAATATGACGGCTGTCAATGTTGCCCTGATTCGAGATACCAAGTG AATTCTTTCTTAATCCTTTAATAGTCCACAGTAATATTGTCCTGAAGAGGGTACATTGGATTTTAATTTTGCTTTCAATATGACGGCTGTCAATGTTGCCCTGATTCGAGATACCAAGTG AATTCTTTCTTAATCCTTTAATAGTCCACAGTAATATTGTCCTGAAGAGGGTACATTTGATTTTAATTTTGCTTTCAATATGACGGCTGTCAATGTTGCCCTGATTCGAGATACCAAGTG AATTCTTTCTTAATCCTTTAATAGTCCACAGTAATATTGTCCTGAAGAGGGTACATTTGATTTTAATTTTGCTTTCAATATGACGGCTGTCAATGTTGCCCTGATTCGAGATACAAAGTG AATTCTTTCTTAATCCTTTAATAGTCCACAGTAATATTGTCCTGAAGAGGGTACATTTGATTTTAATTTTGCTTTCAATATGACGGCTGTCAATGTTGCCCAGATTCGAGATACAAAGTG AATTCTTTCTTAATCCTTTAATAGTACACAGTAATATTGTCCTGAAGAGGGTACATTTGATTTTAATTTTGCTTTCAATATGACGGCTGTCAATGTTGCCCAGATTCGAGATACAAAGTG AATTCTTTCTTAATCCTTTAATAGTACCCAGTAATATTGTCCTGAAGAGGGTACATTTGATTTTAATTTTGCTTTCAATATGACGGCTGTCAATGTTGCCCAGATTCGAGATACAAAGTG AATTCTTTCTTAATCCTTTAATAGTACCCAGTAATAATGTCCTGAAGAGGGTACATTTGATTTTAATTTTGCTTTCAATATGACGGCTGTCAATGTTGCCCAGATTCGAGATACAAAGTG