Motifs in DNA Sequence

This is a FREE and simple perl script which can be used to find the motifs in a DNA sequence. This script runs both on windows and linux.

Perl Scripts for Bioinformatics to find the motifs in a DNA sequence

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

# This script will find the motifs in a 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\#################### motifs in DNA SEQUENCE #################### \n\n"; print "This script find the motifs in a DNA sequence\n\n"; print "ENTER THE FILENAME OF THE DNA SEQUENCE:= "; $dnafilename = <STDIN>; chomp $dnafilename; unless ( open(dnafilename, $dnafilename) ) { print "Cannot open file \"$dnafilename\"\n\n"; exit; } @protein = <dnafilename>; close dnafilename; $protein = join( '', @protein); $protein =~ s/\s//g; do { print "ENTER A MOTIF {Sequence} TO SEARCH FOR := "; $motif = <STDIN>; chomp $motif; if ( $protein =~ /$motif/ ) { print "Found it!\n\n"; exit; } else { print "Not found.\n\n"; exit; } } until ( $motif =~ /^\s*$/ );

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

AATTCATTTTTAATCCTTTAATAGTCCACAGTAATATTGTCCTAAAGAGGGTACATTGG ATTTTAATTTTGCTTTCAATATGACGGCTGTCAATGTTGCCCTGATTCGTGATACCAAGTG GCTGACTTTAGAAGTCTGTAGAGAATTTCAGAGAGGAACTTGCTCTCGAGCTGATGCAGATT GCAAGTTTGCCCATCCACCAAGAGTTTGCCATGTGGAAAATGGTCGTGTGGTGGCCTGTTTTG ATTCTCTAAAGGGTCGGTGTACCCGAGAGAACTGCAAGTACCTTCACCCTCCTCCACACTTAA AAACGCAGCTGGAGATTAATGGGCGGAACAATCTGATTCAACAGAAGACTGCCGCAGCCATGTT CGCCCAGCAGATGCAGCTTATGCTCCAAAACGCTCAAATGTCATCACTTGGTTCTTTTCCTATG ACTCCATCAATTCCAGCTAATCCTCCCATGGCTTTCAATCCTTACATACCACATCCTGGGATGGG CCTCGTTCCTGCAGAACTTGTACCAAATACACCTGTTCTGATTCCTGGAAACCCACCTCTTGCAAT GCCAGGAGCTGTTGGCCCAAAACTGATGCGTTCAGATAAACTGGAGGTTTGCCGA

Result for motifs.pl

perl motifs.pl #################### motifs in DNA SEQUENCE#################### This script find the motifs in a DNA sequence ENTER THE FILENAME OF THE DNA SEQUENCE:= ../bioseq/dnafile.txt ENTER A MOTIF {Sequence} TO SEARCH FOR := azs Not found. ============================================================================== perl motifs.pl #################### motifs in DNA SEQUENCE#################### This script find the motifs in a DNA sequence ENTER THE FILENAME OF THE DNA SEQUENCE:= ../bioseq/dnafile.txt ENTER A MOTIF {Sequence} TO SEARCH FOR := TCGGTGTACCCGAGAGAACTGCAAGTACCTTCA Found it!