Frequency of Nucleotide

This is a FREE and simple perl script which can be used to to count the number of Adenine, Thymine, Guanine and Cytosine in your DNA Sequence. This script calculates the frequency of Nucleotide. This script runs both on windows and linux.

Perl Scripts for Bioinformatics to count the number of Adenine, Thymine, Guanine and Cytosine in your DNA Sequence

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

# This script will count the number of Adenine, Thymine, Guanine and Cytosine in your DNA Sequence # While executing this script it asks for the file name of the DNA sequence. If the sequence file is not available in the same directory of this script, enter the name of the file along with the path. eg.In windows: c:\dnafile.txt, In Linux: /home/user/sequence/dnafile.txt print "\n\n\t\#################### FREQUENCY OF NUCLIOTIDE #################### \n\n"; print "This script will count the number of Adenine, Thymine, Guanine and Cytosine in your DNA Sequence\n\n"; print "ENTER THE FILENAME OF THE DNA SEQUENCE:= "; $dna_filename = <STDIN>; chomp $dna_filename; unless ( open(DNAFILE, $dna_filename) ) { print "Sorry the file does not exist!!! \n"; print "Cannot open file \"$dna_filename\"\n"; die; } @DNA = <DNAFILE>; close DNAFILE; $DNA = join( '', @DNA); print " \n The original DNA file is:\n $DNA \n"; $DNA =~ s/\s//g; @DNA = split( '', $DNA ); $count_of_A = 0; $count_of_C = 0; $count_of_G = 0; $count_of_T = 0; $errors = 0; foreach $base (@DNA) { if ( $base eq 'a' ) { ++$count_of_A; } elsif ( $base eq 'c' ) { ++$count_of_C; } elsif ( $base eq 'g' ) { ++$count_of_G; } elsif ( $base eq 't' ) { ++$count_of_T; } elsif ( $base eq 'T' ) { ++$count_of_T; } elsif ( $base eq 'C' ) { ++$count_of_C; } elsif ( $base eq 'A' ) { ++$count_of_A; } elsif ( $base eq 'G' ) { ++$count_of_G; } else { print "Error - Unknown base: $base\n"; ++$errors; } } print "Adenine = $count_of_A\n"; print "Cytosine = $count_of_C\n"; print "Guanine = $count_of_G\n"; print "Thymine = $count_of_T\n"; if ($errors) { print "There were $errors unrecognized bases.\n"; }

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

AATTCATTTTTAATCCTTTAATAGTCCACAGTAATATTGTCCTAAAGAGGGTACATTGG ATTTTAATTTTGCTTTCAATATGACGGCTGTCAATGTTGCCCTGATTCGTGATACCAAGTG GCTGACTTTAGAAGTCTGTAGAGAATTTCAGAGAGGAACTTGCTCTCGAGCTGATGCAGATT GCAAGTTTGCCCATCCACCAAGAGTTTGCCATGTGGAAAATGGTCGTGTGGTGGCCTGTTTTG ATTCTCTAAAGGGTCGGTGTACCCGAGAGAACTGCAAGTACCTTCACCCTCCTCCACACTTAA AAACGCAGCTGGAGATTAATGGGCGGAACAATCTGATTCAACAGAAGACTGCCGCAGCCATGTT CGCCCAGCAGATGCAGCTTATGCTCCAAAACGCTCAAATGTCATCACTTGGTTCTTTTCCTATG ACTCCATCAATTCCAGCTAATCCTCCCATGGCTTTCAATCCTTACATACCACATCCTGGGATGGG CCTCGTTCCTGCAGAACTTGTACCAAATACACCTGTTCTGATTCCTGGAAACCCACCTCTTGCAAT GCCAGGAGCTGTTGGCCCAAAACTGATGCGTTCAGATAAACTGGAGGTTTGCCGA

Result for dnafrequency.pl

>> perl dnafrequency.pl #################### FREQUENCY OF NUCLIOTIDE #################### This script will count the number of Adenine, Thymine, Guanine and Cytosine in your DNA Sequence ENTER THE FILENAME OF THE DNA SEQUENCE:= ../bioseq/dnafile.txt The original DNA file is: AATTCATTTTTAATCCTTTAATAGTCCACAGTAATATTGTCCTAAAGAGGGTACATTGG ATTTTAATTTTGCTTTCAATATGACGGCTGTCAATGTTGCCCTGATTCGTGATACCAAGTG GCTGACTTTAGAAGTCTGTAGAGAATTTCAGAGAGGAACTTGCTCTCGAGCTGATGCAGATT GCAAGTTTGCCCATCCACCAAGAGTTTGCCATGTGGAAAATGGTCGTGTGGTGGCCTGTTTTG ATTCTCTAAAGGGTCGGTGTACCCGAGAGAACTGCAAGTACCTTCACCCTCCTCCACACTTAA AAACGCAGCTGGAGATTAATGGGCGGAACAATCTGATTCAACAGAAGACTGCCGCAGCCATGTT CGCCCAGCAGATGCAGCTTATGCTCCAAAACGCTCAAATGTCATCACTTGGTTCTTTTCCTATG ACTCCATCAATTCCAGCTAATCCTCCCATGGCTTTCAATCCTTACATACCACATCCTGGGATGGG CCTCGTTCCTGCAGAACTTGTACCAAATACACCTGTTCTGATTCCTGGAAACCCACCTCTTGCAAT GCCAGGAGCTGTTGGCCCAAAACTGATGCGTTCAGATAAACTGGAGGTTTGCCGA