Two suggestions
  1. You do not need the for loop at all, you are merely counting to 30 and doing something once when you reach a magic number. This is particularly true if the starting dna sequence is greater than 30 bases.
  2. A look up table would be faster then an "until we get a different answer", this is particularly true if you are going to mutate your starting sequence repeatedly.
Try this for example 
#!/usr/bin/perl 

use strict;
use warnings;

print "The DNA sequence is : \n" ;
my $seq = 'AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA';

print "$seq \n";
mutate ($seq);
exit;

sub mutate{
        my($dna) = shift;
        my $position = randposition($dna);
        print " mutation at  base position ". ($position+1) . "\n";
        my $nucleotide = randombase(substr($dna,$position,1));
        substr($dna, $position, 1, $nucleotide);
        print "$dna\n";
}

sub randposition{
        my($sequence) = @_;
        return int rand length($sequence);
}

sub randombase{
        my $base=shift;
        my(%nucleo)=(   'A'=>['T','C','G'],
                        'T'=>['A','C','G'],
                        'C'=>['A','T','G'],
                        'G'=>['A','T','G'],
                    );
        return $nucleo{$base}[rand(@{$nucleo{$base}})];
}

[download]
print "Good ",qw(night morning afternoon evening)[(localtime)[2]/6]," fellow monks."

In reply to Re: Help regarding the outout of the program by Utilitarian
in thread Help regarding the outout of the program by minnie

Title:
Use:  <p> text here (a paragraph) </p>
and:  <code> code here </code>
to format your post, it's "PerlMonks-approved HTML":


  • Posts are HTML formatted. Put <p> </p> tags around your paragraphs. Put <code> </code> tags around your code and data!
  • Titles consisting of a single word are discouraged, and in most cases are disallowed outright.
  • Read Where should I post X? if you're not absolutely sure you're posting in the right place.
  • Please read these before you post! —
  • Posts may use any of the Perl Monks Approved HTML tags:
    a, abbr, b, big, blockquote, br, caption, center, col, colgroup, dd, del, details, div, dl, dt, em, font, h1, h2, h3, h4, h5, h6, hr, i, ins, li, ol, p, pre, readmore, small, span, spoiler, strike, strong, sub, summary, sup, table, tbody, td, tfoot, th, thead, tr, tt, u, ul, wbr
  • You may need to use entities for some characters, as follows. (Exception: Within code tags, you can put the characters literally.)
            For:     Use:
    & &amp;
    < &lt;
    > &gt;
    [ &#91;
    ] &#93;
  • Link using PerlMonks shortcuts! What shortcuts can I use for linking?
  • See Writeup Formatting Tips and other pages linked from there for more info.