DNA Sequence to Protein Sequence

Copy the below code and save it as " dna2protein.pl " on your system.

# This script will convert your DNA sequence to PROTEIN 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\#################### DNA 2 PROTEIN #################### \n\n"; print "This script will convert your DNA sequence to PROTEIN Sequence\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"; } @DNA = <DNAFILE>; close DNAFILE; $DNA = join( '', @DNA); print " \nThe original DNA file is:\n$DNA \n"; $DNA =~ s/\s//g; my $protein=''; my $codon; for(my $i=0;$i<(length($DNA)-2);$i+=3) { $codon=substr($DNA,$i,3); $protein.=&codon2aa($codon); } print "The translated protein is :\n$protein\n"; <STDIN>; sub codon2aa{ my($codon)=@_; $codon=uc $codon; my(%g)=('TCA'=>'S','TCC'=>'S','TCG'=>'S','TCT'=>'S','TTC'=>'F','TTT'=>'F','TTA'=>'L','TTG'=>'L','TAC'=>'Y','TAT'=>'Y','TAA'=>'_','TAG'=>'_','TGC'=>'C','TGT'=>'C','TGA'=>'_','TGG'=>'W','CTA'=>'L','CTC'=>'L','CTG'=>'L','CTT'=>'L','CCA'=>'P','CCC'=>'P','CCG'=>'P','CCT'=>'P','CAC'=>'H','CAT'=>'H','CAA'=>'Q','CAG'=>'Q','CGA'=>'R','CGC'=>'R','CGG'=>'R','CGT'=>'R','ATA'=>'I','ATC'=>'I','ATT'=>'I','ATG'=>'M','ACA'=>'T','ACC'=>'T','ACG'=>'T','ACT'=>'T','AAC'=>'N','AAT'=>'N','AAA'=>'K','AAG'=>'K','AGC'=>'S','AGT'=>'S','AGA'=>'R','AGG'=>'R','GTA'=>'V','GTC'=>'V','GTG'=>'V','GTT'=>'V','GCA'=>'A','GCC'=>'A','GCG'=>'A','GCT'=>'A','GAC'=>'D','GAT'=>'D','GAA'=>'E','GAG'=>'E','GGA'=>'G','GGC'=>'G','GGG'=>'G','GGT'=>'G'); if(exists $g{$codon}) { return $g{$codon}; } else { print STDERR "Bad codon \"$codon\"!!\n"; exit; } }

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

AATTCATTTTTAATCCTTTAATAGTCCACAGTAATATTGTCCTAAAGAGGGTACATTGG ATTTTAATTTTGCTTTCAATATGACGGCTGTCAATGTTGCCCTGATTCGTGATACCAAGTG GCTGACTTTAGAAGTCTGTAGAGAATTTCAGAGAGGAACTTGCTCTCGAGCTGATGCAGATT GCAAGTTTGCCCATCCACCAAGAGTTTGCCATGTGGAAAATGGTCGTGTGGTGGCCTGTTTTG ATTCTCTAAAGGGTCGGTGTACCCGAGAGAACTGCAAGTACCTTCACCCTCCTCCACACTTAA AAACGCAGCTGGAGATTAATGGGCGGAACAATCTGATTCAACAGAAGACTGCCGCAGCCATGTT CGCCCAGCAGATGCAGCTTATGCTCCAAAACGCTCAAATGTCATCACTTGGTTCTTTTCCTATG ACTCCATCAATTCCAGCTAATCCTCCCATGGCTTTCAATCCTTACATACCACATCCTGGGATGGG CCTCGTTCCTGCAGAACTTGTACCAAATACACCTGTTCTGATTCCTGGAAACCCACCTCTTGCAAT GCCAGGAGCTGTTGGCCCAAAACTGATGCGTTCAGATAAACTGGAGGTTTGCCGA

Result for dna2protein.pl

>> perl dna2protien.pl #################### DNA 2 PROTEIN #################### This script will convert your DNA sequence to PROTEIN 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 The translated protein is : NSFLIL__STVILS_RGYIGF_FCFQYDGCQCCPDS_YQVADFRSL_RISERNLLSS_CRLQVCPSTKSLPCGKWSCGGLF_FSKGSVYPRELQVPSPSSTLKNAAGD_WAEQSDSTEDCRSHVRPADAAYAPKRSNVITWFFSYDSINSS_SSHGFQSLHTTSWDGPRSCRTCTKYTCSDSWKPTSCNARSCWPKTDAFR_TGGLP