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<h1>Computer Assisted Simulation of DNA using Linux and
Perl</h1>
<h4>ArticleCategory: [Choose a category, do not translate
this]</h4>
SoftwareDevelopment
<h4>AuthorImage:[Here we need a little image from you]</h4>
<img src="../../common/images2/CarlosAndresPerez.jpg" alt="La Foto" width="127" height="159">
<h4>TranslationInfo:[Author + translation history. mailto: or
http://homepage]</h4>
<p>original in es <a href="nospam:caperez@usc.edu.co">Carlos
Andrés Pérez</a></p>
<p>en to es <a href="nospam:caperez@usc.edu.co">Carlos
Andrés Pérez</a></p>
<h4>AboutTheAuthor:[A small biography about the author]</h4>
Carlos Andrés Pérez is specialist in Molecular
Simulation, Candidate to Doctor in Biotechnology. Technical
advisor of the Grupo de Investigación en
Educación Virtual (GIEV) - Research Group in Virtual
Learning. Address: Universidad Santiago de Cali, Calle 5ª
carrera 62 Campus Pampalinda, Cali – Colombia.
<h4>Abstract:[Here you write a little summary]</h4>
This article shows a way to generate “n” DNA
sequences with “s” nucleotides, in a random way
using Perl programs. In contrast with other programs where
DNA sequences are processed as text chains, this article
proposes to work with them as arrays. Even with the random
generation of the sequences, when we do the statistical
analysis of the media fraction of the identical nucleotides
that are placed in the same comparative position, we obtain
values similar to 0.25.
<h4>ArticleIllustration:[This is the title picture for your
article]</h4>
<img src="../../common/images2/article388.jpg" alt="[Illustration]" hspace="10" width="137" height="180">
<h4>ArticleBody:[The article body]</h4>
<h2>Computer simulation</h2>
<p>The scientific research is focused on the study and
understanding of processes in nature. The research has been
done using experimental observation and theoretical modeling,
which, for a long time has been dedicated to exposition and
development of equations. But many of these equations can't be
solved analytically or numerically because of technical aspects
or the impossibility of representing nature.</p>
<p>The ever growing development of computing sciences leaves us
to reach the natural phenomenons through software programs that
can replace the mathematical equations for describing natural
systems. These programs ease the introduction of random
variables that ease the reproduction of biological and physical
processes in the computer, finding deterministic aspects in the
simulations, that can be translated after wards into laws.</p>
<h2>Why perl?</h2>
<p>Perl (Practical Extraction and Report Language), is an
structured language that handles data of scalar, list, array,
hashes and files types. It is already versatile in its
applicability, because it is easy to generate functions that
can be evaluated with any data type, besides to its capability
of integration in databases, dynamic websites and operating
systems like Linux, assisting the end user with common
tasks.</p>
<p>Perl is very attractive as analytic tool because its syntax
allows us to work with very similar structures to Mathematica,
a powerful symbolic language (<a href=
"http://www.xahlee.org/PerlMathematica_dir/perlMathematica.html">
http://www.xahlee.org/PerlMathematica_dir/perlMathematica.html</a>
), and its modules can be integrate with C, GTK, GGI, GGL
libraries, adding the capabilities of integrating programs in a
single language.</p>
<p>There are several programs with a big advantage in the data
management, structured in a mathematical way of programming.
But these are commercial software packages and this limits its
reproduction and improvement. At the same time they are very
restrictive when communicating with other languages.</p>
<p>Perl doesn't limit the data size, it depends on the memory
capabilities and the recursive resources. The number of hash
tables used in associative arrays isn't also limited.</p>
<p>In this article every DNA chain has been represented as a
vector. We can use the PDL module (Perl Data Language, (<a
href=
"http://pdl.sourceforge.net/WWW-old/index_es.html">http://pdl.sourceforge.net/WWW-old/index_es.html</a>
), which is oriented to the numeric processing of data through
n-dimensional matrices, but we have trouble defining each
vector element as a nucleotide, because the “pdl”
function only handles numeric orders. For that reason we
proceed to use the Perl basic functions for handling arrays,
anyway this doesn't limits the possibility of representing each
nucleotide as a number.</p>
<h2>Random sequences</h2>
The program, let us generate “n” DNA chains
composed of “s” nucleotides. Each chain has the
same length and its components are nucleotides randomly chosen.
The program converts the scalar list passed as parameter by the
Dumper function in a Perl chain that describes the data
structure, so we can visualize each vector. <br>
<br>
<pre class="code">
#!/usr/bin/perl
# Use the module Data::Dumper
use Data::Dumper;
# In $var1 the sequences number is stored, in $var2 the chain length.
print "Enter the number of random sequences to be generated\n";
$var1 = <STDIN>;
print "Enter the number of nucleotides per sequence\n";
$var2 = <STDIN>;
# In aleatorio we define the array @ns that contains the nucleotides,
# $lon is the local variable that stores the number of nucleotides
# $col is the local variable that stores the number of
# sequences
sub aleatorio {
local @ns = (a,g,c,t);
local $lon = $_[1];
local $col = $_[0];
# We define an empty array @a to store the vectors.
@a = ();
# The variables that indicate the vectors and its componnent?s positions.
local $i = 0;
local $u = 0;
while ($u <= $col - 1 && $i <= $lon - 1) {
# $result is the variable that stores the random election of every of the
# nucleotides.
$result = @ns[int(rand(4))];
# Add nucleotides and store the chains that contains them.
$a[$u][$i] = $result;
$i = $i + 1;
if ($i == $lon ) {
$u = $u + 1;
$i = 0;
}
}
return @a;
}
#Show in the creen every vector and its components.
print Dumper(&aleatorio($var1,$var2));
# Define positions and inicial vectors used to compare
# if they have identical nucleotides in the same positions.
$k = 0;
$count = 0;
$s1 = 0;
$s2 = 1;
while ($s1 <= $col - 2 && $s2 <= $col - 1 && $k <= $lon - 1 ) {
# If they are identical $count increases in 1.
if ($a[$s1][$k] eq $a[$s2][$k]) {
$count = $count + 1;
}
# $k indicates nucleotides in the vector, $s1 and $s2 are the vectors being compared.
# If $k value is the same at the nucleotides number is a flag
# that the comparation has finished.
$k = $k + 1;
if($k == $lon ) {
$k = 0;
$s2 = $s2 +1;
}
# If $s2 is the same than $col, we know that one of the vectors has been
# compared with the others.
if ($s2 == $col ) {
$k = 0;
$s1 = $s1 + 1;
$s2 = $s1 + 1 ;
}
}
# We determine $pvalue
# which shows the number of comparisons.
for ($p = $col - 1, $r = $col -2; $r >= 0 ; $r--){
$p+= $r;
}
# The results are shown.
print "The number of identical nucleotides is: $count\n";
print "The number of comparisons is: $p\n";
$y = $count/$p;
# In $cor we store the media fraction value of
# identical nucleotides in the same position
#during the comparison.
$cor = $y/$lon;
print "The media fraction of nucleotides appearing in the same position is: $cor";
</pre>
<p>Estimating the $cor value for 10 sequences of 30, 50, 70 and
90 nucleotides we get the following results: 0.2340, 0.26,
0.26031, 0.2661.</p>
<p>For 40 sequences of 100, 200, 300 and 500 nucleotides we get
the following values of $cor: 0.2507, 0.2482, 0.2480,
0.2489.</p>
<p><br>
</p>
<p>According to that we conclude that for “n”
number of DNA sequences with “s” nucleotides and
randomly generated, show a media fraction of identical
nucleotides that are in the same position around 0.25.</p>
<h2>Bibliography</h2>
<ul>
<li><a href=
"http://bioperl.org/">http://bioperl.org/</a></li>
<li><a href=
"http://pdl.perl.org/index_es.html">http://pdl.perl.org/index_es.html</a></li>
<li><a href=
"http://www.unix.org.ua/orelly/perl/prog3/">http://www.unix.org.ua/orelly/perl/prog3/</a></li>
<li><a href=
"http://www.xahlee.org/PerlMathematica_dir/Matica.html">http://www.xahlee.org/PerlMathematica_dir/Matica.html</a></li>
<li>Examples of file manipulation in perl created by Dr.
Antonio J. Pérez Pulido for the Magister in
Bioinformatics of the Andalucía International
University.</li>
<li><a href="../April2005/article374.shtml">linuxfocus.org
April2005/article374</a></li>
</ul>
<h2>File download</h2>
<a href="../../common/src2/article388_ADNaleatorio_pl.txt">Perl
source code: ADNaleatorio_pl.txt</a>
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