View source for 7) Aligning two protein sequences

<p><strong>This one compares two sequence, which user input. But is not designed for global alignment.&nbsp;</strong></p>

<p>#!/usr/bin/perl<br />
use strict;<br />
use warnings;</p>

<p>&nbsp; <strong>my $dna1 = &lt;STDIN&gt;;</strong><br />
&nbsp; chomp($dna1);<br />
&nbsp; &nbsp;my @string1 = split (&#39;&#39;, $dna1);<br />
&nbsp; &nbsp;<strong>my $len1 = length $dna1;</strong></p>

<p>&nbsp; <strong>my $dna2 = &lt;STDIN&gt;;</strong><br />
&nbsp; chomp ($dna2);<br />
&nbsp; my @string2 = split (&#39;&#39;, $dna2);<br />
&nbsp; <strong>my $len2 = length $dna2;</strong></p>

<p>sub max {<br />
&nbsp; &nbsp; my ($max, @vars) = @_;<br />
&nbsp; for (@vars) {<br />
&nbsp; &nbsp;<strong> &nbsp;$max = $_ if $_ &gt; $max;</strong><br />
&nbsp; &nbsp; }<br />
&nbsp;return $max;<br />
}</p>

<p><strong>&nbsp;my $stlen = max ($len1, $len2);</strong></p>

<p>&nbsp; <strong>foreach (my $i =0; $i &lt; $stlen; $i++) </strong>{<br />
&nbsp; &nbsp; &nbsp; if ( $string1[$i] eq $string2[$i] ) {<br />
&nbsp; &nbsp; &nbsp;print &quot; $string1[$i] = $string2[$i]\n&quot;;}<br />
&nbsp; &nbsp;else<br />
&nbsp; &nbsp; &nbsp; &nbsp; { print &quot;$string1[$i] x $string2[$i]\n&quot;; }<br />
}<br />
&nbsp;</p>

<p><strong>The output result sample is:</strong>&nbsp;</p>

<p>MKRRRLLYYILEUGNMCG<br />
KKKRRLLYVILEUGNNNG<br />
&nbsp;M x K<br />
&nbsp;K = K<br />
&nbsp;R x K<br />
&nbsp;R = R<br />
&nbsp;R = R<br />
&nbsp;L = L<br />
&nbsp;L = L<br />
&nbsp;Y = Y<br />
&nbsp;Y x V<br />
&nbsp;I = I<br />
&nbsp;L = L<br />
&nbsp;E = E<br />
&nbsp;U = U<br />
&nbsp;G = G<br />
&nbsp;N = N<br />
&nbsp;M x N<br />
&nbsp;C x N<br />
&nbsp;G = G<br />
&nbsp;</p>