Perl: DNA sequence manipulation

Abstract: Truncation, reverse-complementary, translation of DNA sequence.

Two methods for DNA/protein manipulations with Bio-perl module or self-defined subroutines are present. Here is a Perl script to show how finish those manipulations of DNA/protein sequences using Bio-perl.

#! /usr/bin/perl -w

use strict;

use warnings;

use Bio::SeqIO;

use Bio::Perl;

#

my $DNA='CTTCATGTGATTGAGGATTTCATTGACCAGGACACCCCCTTGGAGCCTA';

print "Original DNA sequence: $DNA\n";

#objected-DNA

my $seq_obj=Bio::Seq->new(-seq=>$DNA, -display_id=>'test_DNA', -alphabet=>'DNA');

#DNA manipulations

my $seq_len=$seq_obj->length();

print "Length of DNA sequence: $seq_len\n";

my $seq_trunc=$seq_obj->subseq(5, 10);

print "Truncated DNA sequence at 5-10: $seq_trunc\n";

#protein manipulations

my $pro_obj=$seq_obj->translate();

my $pro_seq=$pro_obj->seq();

my $pro_len=$pro_obj->length();

print "Translation of DNA sequence into protein: $pro_seq\n";

print "Number of amino acid sequence: $pro_len\n";

#reverse-complementary DNA

my $rev_obj=Bio::Perl::revcom($DNA);

my $rev_seq=$rev_obj->seq();

print "Reversed-complementary sequence: $rev_seq\n";

Here is the output:

Original DNA sequence: CTTCATGTGATTGAGGATTTCATTGACCAGGACACCCCCTTGGAGCCTA

Length of DNA sequence: 49

Truncated DNA sequence at 5-10: ATGTGA

Translation of DNA sequence into protein: LHVIEDFIDQDTPLEP

Number of amino acid sequence: 16

Reversed-complementary sequence: TAGGCTCCAAGGGGGTGTCCTGGTCAATGAAATCCTCAATCACATGAAG

OK

I give another method known as DNA_translation() to translate DNA sequence into protein sequence without Bio-Perl modules. This function ca meet your special requirements for protein translation

sub DNA_translation{

my ($seq)=@_;

#separate DNA sequence by three letters

my @three_code=$seq=~/.../sg;

#Genetic code

#(Phe/F) Phenylalanine #(Trp/W) Tryptophan #(Gln/Q) Glutamine #(Asn/N) Asparagine

#(Asp/D) Aspartic acid #(Glu/E) Glutamic acid #(Arg/R) Arginine #(Lys/K) Lysine

#(Ser/S) Serine #(Tyr/Y) Tyrosine #(Cys/C) Cysteine #(Leu/L) Leucine

#(Pro/P) Proline #(His/H) Histidine #(Ile/I) Isoleucine #(Thr/T) Threonine

#(Ser/S) Serine #(Met/M) Methionine #(Val/V) Valine #(Ala/A) Alanine #(Gly/G) Glycine

my %genetic_code=( TAA=>'.', TGA=>'.', TAG=>'.', ATG=>'M', TGG=>'W',

CGT=>'R', CGC=>'R', CGA=>'R', CGG=>'R',AGA=>'R',AGG=>'R',

TTA=>'L', TTG=>'L', CTT=>'L', CTC=>'L', CTA=>'L', CTG=>'L',

TCT=>'S', TCC=>'S', TCA=>'S', TCG=>'S', AGT=>'S', AGC=>'S',

GCC=>'A', GCT=>'A', GCA=>'A', GCG=>'A', GGT=>'G', GGC=>'G', GGA=>'G', GGG=>'G',

CCT=>'P', CCC=>'P', CCA=>'P', CCG=>'P', GTT=>'V', GTC=>'V', GTA=>'V', GTG=>'V',

ACT=>'T', ACC=>'T', ACA=>'T', ACG=>'T', ATT=>'I', ATC=>'I', ATA=>'I', AAA=>'K', AAG=>'K',

GAA=>'E', GAG=>'E', GAT=>'D', GAC=>'D', TAT=>'Y', TAC=>'Y', TGT=>'C', TGC=>'C',

TTT=>'F', TTC=>'F', CAT=>'H', CAC=>'H', CAA=>'Q', CAG=>'Q', AAT=>'N', AAC=>'N',

);

#tranlation

my @aa;

foreach my $tc(@three_code){

my $amino_acid= (exists $genetic_code{$tc}) ? $genetic_code{$tc} : '*';

push(@aa, $amino_acid);

}

my $aa_seq=join("", @aa);

print "$aa_seq\n";

return($aa_seq);

}

Here is another subroutine for reversed-complementary DNA

sub reverse_complement {

my $dna_seq = shift;

# reverse the DNA sequence

my $revcom = reverse($dna_seq);

# complement the reversed DNA sequence

$revcom =~ tr/ABCDGHMNRSTUVWXYabcdghmnrstuvwxy/TVGHCDKNYSAABWXRtvghcdknysaabwxr/;

return ($revcom);

}

Writing data: 2013.08.10