View source for KSH HW2 Translation of DNA sequences into Amino acids

<p>I tried to make a code to translate DNA sequences into amino acids&nbsp;using Perl program.</p>

<h3>Foreach loop<sup>1)</sup></h3>

<p>First, I learned about Perl&nbsp;foreach loop.</p>

<p>Perl foreach loop iterates over a list value and sets the control variable to be each element of the list in turn</p>

<p>The basic form is like this</p>

<p>foreach&nbsp;var (list) {</p>

<p>&nbsp;</p>

<p>}</p>

<p>Example</p>

<pre>
<span style="color:rgb(136,0,0)">#!/usr/local/bin/perl</span>
 
<span style="color:rgb(0,102,102)">@list</span> <span style="color:rgb(102,102,0)">=</span> <span style="color:rgb(102,102,0)">(</span><span style="color:rgb(0,102,102)">2</span><span style="color:rgb(102,102,0)">,</span> <span style="color:rgb(0,102,102)">20</span><span style="color:rgb(102,102,0)">,</span> <span style="color:rgb(0,102,102)">30</span><span style="color:rgb(102,102,0)">,</span> <span style="color:rgb(0,102,102)">40</span><span style="color:rgb(102,102,0)">,</span> <span style="color:rgb(0,102,102)">50</span><span style="color:rgb(102,102,0)">);</span>

<span style="color:rgb(136,0,0)"># foreach loop execution</span>
<span style="color:rgb(0,0,136)">foreach</span> $a <span style="color:rgb(102,102,0)">(</span><span style="color:rgb(0,102,102)">@list</span><span style="color:rgb(102,102,0)">){</span>
    <span style="color:rgb(0,0,136)">print</span> <span style="color:rgb(0,136,0)">&quot;value of a: $a\n&quot;</span><span style="color:rgb(102,102,0)">;</span>
<span style="color:rgb(102,102,0)">}</span></pre>

<p><span style="color:rgb(102,102,0)">The result is</span></p>

<pre>
value of a: 2
value of a: 20
value of a: 30
value of a: 40
value of a: 50
</pre>

<h3>Perl Script to convert DNA to Protein</h3>

<p>To make a new object and save to a file, write down</p>

<p>1. use Bio::Seq;</p>

<p>&nbsp;&nbsp; use Bio::SeqIO;</p>

<p>When&nbsp;we make a new object,&nbsp;we always&nbsp;have to use this method (method is a function)</p>

<p>2. new()</p>

<p>3. -&gt; : Method call sign</p>

<p>We have to use these arguments to read codon and&nbsp;save it (Argument is a variable to use function or command)</p>

<p>4. -seq, -alphabet, -file, -format</p>

<p>5. =&gt; : To assign argument value<br />
&nbsp;</p>

<p>6. -alphabet argument has one value among dna, rna, and protein.</p>

<p>&nbsp;&nbsp;&nbsp;-format argument has &#39;fasta&#39; or &#39;genbank&#39; value</p>

<p>7. Translation method:</p>

<p>&nbsp;&nbsp;&nbsp;$argument name = $object name-&gt;translate;</p>

<p>8. Print method:</p>

<p>&nbsp;&nbsp; Print $argument name -&gt;seq, &quot;\n&quot;;</p>

<p>Example<sup>2)</sup></p>

<p>use Bio::Seq;</p>

<p>use Bio::SeqIO;</p>

<p>@bases = (&quot;a&quot;,&quot;t&quot;,&quot;g&quot;,&quot;c&quot;);</p>

<p>&nbsp;&nbsp; foreach $first(@bases){</p>

<p>&nbsp;&nbsp;&nbsp;&nbsp; foreach $second(@bases){</p>

<p>&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; foreach $third(@bases){</p>

<p>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; $codon = $first.$second.$third;</p>

<p>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; $seq_codon = Bio::Seq -&gt; new(-seq =&gt; $codon, -alphabet =&gt; &#39;dna&#39;);</p>

<p>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; $aa_letter = $seq_codon -&gt; translate;</p>

<p>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; print &quot;$codon \t&quot;, $aa_letter-&gt;seq, &quot;\t&quot;;</p>

<p>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; }</p>

<p>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; print &quot;\n&quot;;</p>

<p>&nbsp;&nbsp; }</p>

<p>}</p>

<p>$seqio_aa = Bio::SeqIO-&gt;new(-file =&gt; &#39;aa.fas&#39;, -format =&gt; &#39;fasta&#39;);</p>

<p>$seqio_aa = write_seq($aa_letter);</p>

<p>exit;</p>

<h3>Reference</h3>

<p>1) <a href="http://www.tutorialspoint.com/perl/perl_foreach_loop.htm">http://www.tutorialspoint.com/perl/perl_foreach_loop.htm</a></p>

<p>2) This code&nbsp;was originally written by Myeong Seo Yoon and I made a little modification</p>

<p>&nbsp;</p>