Professional Documents
Culture Documents
Submitted by
------------------------------------------------------------------------
(ASHISH THAKUR)
----------------------------------------------------------
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Lovely Professional University, Phagwara
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LOVELY PROFESSIONAL UNIVERSITY, PHAGWARA
DECLARATION
I hereby declare that the project work entitled (“WEBDESIGNING AND
BIOINFORMATICS ALGORITHM”) is an authentic record of my own work carried out
at, Lovely Professional University, as requirements of capstone project for the award of
degree of B.Tech in Biotechnology, Lovely Professional University, Phagwara, under the
guidance of Er.Sree kanth Babu, during August to December,2010.
Name of student:
ASHISH THAKUR
Date:____________
Certified that the above statement made by the student is correct to the best of our
knowledge and belief.
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ACKNOWLEDGEMENT
I owe a great many thanks to a great many people who helped and supported me
during this project.
My deepest thanks to, Er.SREE KANTH BABU (ASSISTANT PROFESSOR)
the guide of the project for guiding and correcting various documents of mine with attention
and care. He has taken pain to go through the project and make necessary correction as and
when needed.
I would also thank my Institution and my faculty members without whom this
project would have been a distant reality.
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INTRODUCTION
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INTRODUCTION TO PROGRAMMING LANGUAGE USED
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What is a computer program?
It's a set of instructions written in a particular programming language that can be read by the
computer. A program can be as simple as the following Perl language program to print
some DNA sequence data onto the computer screen: print
'ACCTGGTAACCCGGAGATTCCAGCT';
The Perl language programs are written and saved in files, which are ways of saving any
kind of data (not only programs) on a computer. Files are organized hierarchically in groups
called folders on Macintosh or Windows systems or directories in Unix or Linux systems.
The terms folder and directory will be used interchangeably.
It's a carefully defined set of rules for how to write computer programs. By learning the
rules of the language, you can write programs that will run on your computer. Programming
languages are similar to our own natural, or spoken languages, such as English, but are
more strictly defined and specific to certain computer systems. With a little bit of training,
it's not difficult to read or write computer programs. In this book you'll write in Perl; there
are many other
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programming languages. A program that a programmer writes is also called source code, or
just source or code. The source code has to be turned into machine language, a special
language the computer can run. It's hard to write or read a machine language program
because it's all binary numbers; it's often called a binary executable.
What is HTML?
HTML Tags
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HTML Documents = Web Pages
The purpose of a web browser (like Internet Explorer or Firefox) is to read HTML
documents and display them as web pages. The browser does not display the HTML tags,
but uses the tags to interpret the content of the page:
<html>
<body>
</body>
</html>
Example Explained
• The text between <html> and </html> describes the web page
• The text between <body> and </body> is the visible page content
• The text between <h1> and </h1> is displayed as a heading
• The text between <p> and </p> is displayed as a paragraph
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.HTM or .HTML File Extension?
When you save an HTML file, you can use either the .htm or the .html file extension. We
use .htm in our examples. It is a habit from the past, when the software only allowed three
letters in file extensions.
HTML, which stands for Hyper Text Markup Language, is the predominant markup
language for web pages. It provides a means to create structured documents by denoting
structural semantics for text such as headings, paragraphs, lists, links, quotes and other
items. It allows images and objects to be embedded and can be used to create interactive
forms. It is written in the form of HTML elements consisting of "tags" surrounded by angle
brackets within the web page content. It can embed scripts in languages such as JavaScript
which affect the behavior of HTML web pages. HTML can also be used to include
Cascading Style Sheets (CSS) to define the appearance and layout of text and other
material. The W3C, maintainer of both HTML and CSS standards, encourages the use of
CSS over explicit presentational markup.
The Hello world program, a common computer program employed for comparing
programming languages, scripting languages and markup languages is made of 9 lines of
code in HTML, albeit Newlines are optional:
<!doctype html>
<html>
<head>
<title>Hello HTML</title>
</head>
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<body>
<p>Hello World!</p>
</body>
</html>
<html>
<head>
While most browsers will "forgive" not including the <html>, <head> or even the <body>
tags, leaving them out can cause problems with some browsers. For XHTML, closing tags
are absolutely required.
Title tags are displayed in the top title bar of the browser.
BUTTON
EXAMPLE
<FORM METHOD="POST" ACTION="someplace/foo.cgi" ENCTYPE="application/x-
www-form-urlencoded">
Computer Experience:<P>
<INPUT TYPE="button" NAME="choice" VALUE="Less than 1">Less than 1 year.<BR>
<INPUT TYPE="button" NAME="choice" VALUE="1 to 5">1-5 years.<BR>
<INPUT TYPE="button" NAME="choice" VALUE="More than 5">More than 5 years.
<P><INPUT TYPE="reset" VALUE="Clear Form">
<INPUT TYPE="submit" VALUE="Submit">
</FORM>
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CHECKBOX
EXAMPLE
<FORM METHOD="POST" ACTION="someplace/foo.cgi"
ENCTYPE="application/x-www-form-urlencoded">
Computer Experience:<BR>
<INPUT TYPE="checkbox" NAME="choice"
VALUE="Less than 1">Less than 1 year.<BR>
<INPUT TYPE="checkbox" NAME="choice"
VALUE="1 to 5">1-5 years.<BR>
<INPUT TYPE="checkbox" NAME="choice"
VALUE="More than 5">More than 5 years.
<BR><INPUT TYPE="reset" VALUE="Clear Form">
<INPUT TYPE="submit" VALUE="Submit">
</FORM>
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FILE
EXAMPLE
<FORM METHOD="POST" ACTION="someplace/foo.cgi"
ENCTYPE="application/x-www-form-urlencoded">
<TABLE>
<TR>
<TD ALIGN="LEFT">Search your drive:
</TR><TR>
<TD ALIGN="LEFT">
<INPUT TYPE="file" NAME="look" ACCEPT="filetype/*" SIZE=25
MAXLENGTH=150>
</TR>
</TABLE>
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<INPUT TYPE="reset" VALUE="Clear Form">
<INPUT TYPE="submit" VALUE="Submit">
</FORM>
INPUT CHECKED
Having an input field checked by default. Can be used with Checkbox or Radio INPUT
TYPES.
EXAMPLE
<FORM METHOD="POST" ACTION="someplace/foo.cgi"
ENCTYPE="application/x-www-form-urlencoded">
Computer Experience:<BR>
<INPUT TYPE="radio" NAME="choice"
VALUE="Less than 1">Less than 1 year.<BR>
<INPUT TYPE="radio" NAME="choice"
VALUE="1 to 5">1-5 years.<BR>
<INPUT CHECKED TYPE="radio" NAME="choice"
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VALUE="More than 5">More than 5 years.
<BR><INPUT TYPE="reset">
<INPUT TYPE="submit" NAME="submit" VALUE="Submit">
</FORM>
PASSWORD
EXAMPLE
<FORM METHOD="POST" ACTION="someplace/foo.cgi"
ENCTYPE="application/x-www-form-urlencoded">
<TABLE>
<TR>
<TD ALIGN="RIGHT" VALIGN="MIDDLE">Name?
<TD ALIGN="LEFT">
<INPUT TYPE="text" NAME="name" VALUE=""
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SIZE="20" MAXLENGTH="150">
</TR> <TR>
<TD ALIGN="RIGHT" VALIGN="MIDDLE">Password?
<TD ALIGN="LEFT">
<INPUT TYPE="password" NAME="password" VALUE=""
SIZE="25" MAXLENGTH="150">
</TR> </TABLE>
<INPUT TYPE="reset" VALUE="Clear Form">
<INPUT TYPE="submit" VALUE="Submit">
</FORM>
RADIO BUTTONS
EXAMPLE
<FORM METHOD="POST" ACTION="someplace/foo.cgi"
ENCTYPE="application/x-www-form-urlencoded">
Computer Experience:<BR>
<INPUT TYPE="radio" NAME="choice"
VALUE="Less than 1">Less than 1 year.<BR>
<INPUT TYPE="radio" NAME="choice"
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VALUE="1 to 5">1-5 years.<BR>
<INPUT TYPE="radio" NAME="choice"
VALUE="More than 5">More than 5 years.
<BR><INPUT TYPE="reset" VALUE="Clear">
<INPUT TYPE="submit" VALUE="submit">
</FORM>
RADIO GRID
EXAMPLE
<FORM METHOD="POST" ACTION="someplace/foo.cgi">
<TR>
<CAPTION="TOP"><B><B>T-Shirt Order</B></CAPTION>
<TD></TD><TD>White</TD><TD>Blue</TD>
</TR>
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<TR>
<TD ALIGN="LEFT">Small</TD>
<TD><INPUT NAME="torder" TYPE="radio" VALUE="smwhite"></TD>
<TD><INPUT NAME="torder" TYPE="radio" VALUE="smblue"></TD>
</TR>
<TR>
<TD ALIGN="LEFT">Medium</TD>
<TD><INPUT NAME="torder" TYPE="radio" VALUE="medwhite"></TD>
<TD><INPUT NAME="torder" TYPE="radio" VALUE="medblue"></TD>
</TR>
<TR>
<TD ALIGN="LEFT">Large</TD>
<TD><INPUT NAME="torder" TYPE="radio" VALUE="lgwhite"></TD>
<TD><INPUT NAME="torder" TYPE="radio" VALUE="lgblue"></TD>
</TR>
<TR>
<TD></TD>
<TD><INPUT TYPE="reset></TD>
<TD><INPUT TYPE="submit" VALUE="Order"></TD>
</TR>
</TABLE>
</FORM>
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MULTIPLE SUBMIT
EXAMPLE
<FORM METHOD="POST" ACTION="mailto:your@address.com"
ENCTYPE="application/x-www-form-urlencoded">
<INPUT TYPE="submit" VALUE="I Loved it!" Name="I loved your page">
<INPUT TYPE="submit" VALUE="It was so-so." Name="Your page is so-so">
</FORM>
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OPTION
EXAMPLE
<FORM METHOD="POST" ACTION="someplace/foo.cgi"
ENCTYPE="application/x-www-form-urlencoded">
Computer Experience:<P>
<SELECT NAME="choice" >
<OPTION VALUE="Less than 1 year.">Less than 1 year.
<OPTION VALUE="1-5 years.">1-5 years.
<OPTION VALUE="More than 5 years.">More than 5 years.
</SELECT>
<BR>
<INPUT TYPE="reset">
<INPUT TYPE="submit" NAME="submit" VALUE="Submit">
</FORM>
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REDIRECT WITHOUT SUBMIT BUTTON
EXAMPLE
<FORM>
Select a destination:<P>
<SELECT MULTIPLE
onChange="window.location=this.options[this.selectedIndex].value;" SIZE="3">
<OPTION VALUE="index.htm">Title Page
<OPTION VALUE="sound.htm">Sound Tags Page
<OPTION VALUE="forms.htm#TOC">Table of Contents
<OPTION VALUE="text.htm">Text Tags Page
</SELECT>
</FORM>
EXAMPLE:-2
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<FORM>
<INPUT type="button" value="To Title Page" onClick="location.href='index.htm'">
</FORM>
TEXTAREA
EXAMPLE
<FORM METHOD="POST" ACTION="someplace/foo.cgi"
ENCTYPE="application/x-www-form-urlencoded">
Tell us about your computer experience:<BR>
<TEXTAREA NAME="choice" ROWS=5 COLS=25>
</TEXTAREA>
<BR>
<INPUT TYPE="reset">
<INPUT TYPE="submit" NAME="submit" VALUE="Submit">
</FORM>
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PERL
(PRACTICAL EXTRACTION AND REPORT LANGUAGE)
The language provides powerful text processing facilities without the arbitrary data length
limits of many contemporary Unix tools, facilitating easy manipulation of text files. It is
also used for graphics programming, system administration, network programming,
applications that require database access and CGI programming on the Web. Perl is
nicknamed "the Swiss Army chainsaw of programming languages" due to its flexibility and
adaptability.
Here is the basic perl program that we'll use to get started.
#!/usr/local/bin/perl
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#
# Program to do the obvious
#
print 'Hello world.'; # Print a message
Substitution
As well as identifying regular expressions Perl can make substitutions based on those
matches. The way to do this is to use the s function which is designed to mimic the way
substitution is done in the vi text editor. Once again the match operator is used, and once
again if it is omitted then the substitution is assumed to take place with the $_ variable.
$sentence =~ s/london/London/
and to do the same thing with the $_ variable just
s/london/London/
Notice that the two regular expressions (london and London) are surrounded by a total of
three slashes. The result of this expression is the number of substitutions made, so it is
either 0 (false) or 1 (true) in this case.
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Options
This example only replaces the first occurrence of the string, and it may be that there will be
more than one such string we want to replace. To make a global substitution the last slash is
followed by a g as follows:
s/london/London/g
which of course works on the $_ variable. Again the expression returns the number of
substitutions made, which is 0 (false) or something greater than 0 (true).
s/[Ll][Oo][Nn][Dd][Oo][Nn]/London/g
but an easier way is to use the i option (for "ignore case"). The expression
s/london/London/gi
will make a global substitution ignoring case. The i option is also used in the basic /.../
regular expression match.
Translation
Most of the special RE codes do not apply in the tr function. For example, the statement
here counts the number of asterisks in the $sentence variable and stores that in the $count
variable.
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However, the dash is still used to mean "between". This statement converts $_ to upper
case.
tr/a-z/A-Z/;
PROGRAM WRITTEN
$seq=$cgi->param("seq");
@opt=$cgi->param("check");
print"content-type: text/html\n\n";
print'<html>
<head>
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<title>SOFTWARE</title> #TITLE LINE REFLECT IN BROWSER
</head>';
print'<body bgcolor="#FFDD75"'; # BACKGROUND COLOR
print "</body></html>";
foreach $opt(@opt) #PERL PROGRAM
if($opt eq 'nucleo')
{
$basecount=($seq=~tr/ATGCatgc//); # COUNTING NUMBER OF
NUCLEOTIDES
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}
if($opt eq 'trans')
{
$seq=~ tr/atgcATGC/tacgTACG/; #TRANSCRIPTION CODE LINE
$seq=~ tr/Tt/Uu/;
my $seq = uc($seq);
my(%genetic_code) = (
#CODON FILE
);
my ($protein) = "";
for(my $i=0;$i<length($seq)-2;$i+=3)
{
$codon = substr($seq,$i,3);
$protein .= $genetic_code{$codon};
}
print "7) TRANSLATION :- $protein<br><br><br><br><br><br>";
print "NOTE:- UNDERSCORE _ SYMBOL IN TRANSLATION SEQUENCE
REPRESENTs THE STOP CODON<br>";
}
}
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WEB PAGE CODING
1) LOGINSCRIPT.HTML
<html>
<title>::BIOINFO::</title>
<head><link rel="shortcut icon" href="favicon.ico">
<img src="top_logo2.png" style="float:right;"/>
</head>
<body bgcolor="#006634">
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<table width="75%" height="10%" border="0">
<tr>
<td bgcolor="006634"><font size="15" color="white"
face="lucida handwriting"><i>CAPSTONE PROJECT</i></font>
</td>
</tr>
</table>
<table width="100%" height="10%">
<tr>
<td background="navigation_bar.png">
<p align="center"/>
<a href="loginscript.html"><b><font
color="white"/><font face="courier new" size="5" decoration:none>HOME|</b></a>
<a href="http://lpu.in/about_lpu.php"><b><font
color="white"/>ABOUT LPU|</b></a>
<a href="projects.html"><b><font
color="white"/>PROJECTS|</b></a>
<a href="contact.html"><b><font
color="white"/>CONTACT US|</b></a>
</td>
</tr>
</table>
<table width="100%" height="20%">
<tr>
<td bgcolor="#FFDD75">
<font face="courier new"><p align="center">WELCOME TO BIOINFO
THIS WEBPAGE IS THE RESULT OF MY PROJECT I DESIGN IT BY USING
HTML(HYPER TEXT MARKUP LANGUAGE),CGI(COMMON GATEWAY
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INTERFACE),PERL(PRACTICAL EXTRACTION AND REPORT LANGUAGE),I
ALSO USE A VIRTUAL SERVER KNOW AS WAMP.WAMP STAND FOR<br>W-
>WINDOWS<br> A->APACHE<br> M->MYSQL<br>P->PHP<br> IT PROVIDES AN
ENVIRONMENT OF SERVER BUT IT ONLY WORK ON YOUR PC ONLY.IT IS
USED TO TEST THE WEBPAGE WHETHER IT WORKS PROPERLY OR NOT,ITS A
TESTING PLATFORM BEFORE PUBLISHING THE WEBSITE.<br>I THANK TO MY
MENTOR <i><b>Er.K.SHREEKANTH BABU</i></b> FOR HIS VALUABLE
GUIDANCE.<br><br>
</font>
<table width="100%" border="1" cellpadding="1" cellspacing="1">
<th bgcolor="#006634"><font face="lucida handwriting" color="white"
size="2">LIST OF BIOINFORMATICS DATABASES/DATABANK ONLINE</th>
<tr>
<td bgcolor="#006634"><a
href="http://www.ncbi.nlm.nih.gov/"><font face="lucida handwriting" size="2"
color="white">NCBI-> NATIONAL CENTER FOR BIOTECHNOLOGY
INFORMATION</td>
<td bgcolor="#006634"><a href="http://www.ebi.ac.uk/"><font
face="lucida handwriting" size="2" color="white">EBI-> EUROPEAN
BIOINFORMATICS INSTITUTE</td>
<td bgcolor="#006634"><a href="http://www.ddbj.nig.ac.jp/"><font
face="lucida handwriting" size="2" color="white">DDBJ-> DNA DATABANK OF
JAPAN</td>
<td bgcolor="#006634"><a
href="http://www.ebi.ac.uk/embl/"><font face="lucida handwriting" size="2"
color="white">EMNEW-> INDEX FOR NEW EMBL NUCLEOTIDES (EBI)</td>
<td bgcolor="#006634"><a
href="http://www.pdb.org/pdb/home/home.do"><font face="lucida handwriting" size="2"
color="white">PDB-> PROTEIN DATA BANK</td>
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<td bgcolor="#006634"><a href="http://expasy.org/"><font
face="lucida handwriting" size="2" color="white">ExPASY-> EXPERT PROTEIN
ANALYSIS SYSTEM</td>
<td bgcolor="#006634"><a href="http://pir.georgetown.edu/"><font
face="lucida handwriting" size="2" color="white">PROTEIN INFORMATION
RESOURCE</td>
</tr>
<th bgcolor="#006634"><font face="lucida handwriting"
color="white" size="2">OTHER LINKS</th>
<tr>
<td bgcolor="#006634"><a
href="https://172.19.2.250/lpuums/loginnew.aspx"><font face="lucida handwriting"
size="2" color="white">UMS LOGIN FOR INSIDE CAMPUS</td>
<td bgcolor="#006634"><a
href="https://202.164.55.98/lpuums/loginnew.aspx"><font face="lucida handwriting"
size="2" color="white">UMS LOGIN FOR OUTSIDE CAMPUS</td>
</tr>
</table>
<br></br><br></br><br></br><br></br><br></br>
<hr>
<font size="2" face="courier new"><p
align="right">DESIGNED BY:- ASHISH THAKUR™ B.TECH-
BIOTECHNOLOGY REG.NO.->3040070009</font></hr>
</body>
</html>
2) PROJECTS.HTML
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<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 1.0 Transitional//EN"
"http://www.w3.org/TR/html1/DTD/html1-transitional.dtd">
<html xmlns="http://www.w3.org/1999/html">
<title>PROJECT</title>
<head>
<form action="/cgi-bin/program.pl">
</head>
<html>
<body bgcolor="#006634">
<table BORDER="0" CELLSPACING="0" CELLPADDING="0"
WIDTH="100%">
<tr>
<td bgcolor="#FFD34F"align="center" valign="center"
WIDTH="100%">
<font face="courier new" size="4">Enter or Copy Paste
Sequence Below:-
<br>
</font>
<center>
<TEXTAREA NAME="seq" ROWS=10
COLS=100></TEXTAREA>
</center>
<table width="40%" height="50%" border="0">
<tr>
<td>
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<P
ALIGN="center"></p>
<INPUT
TYPE="checkbox" name="check" VALUE="nucleo">TOTAL NUMBER OF
NUCLEOTIDES<br><br>
<INPUT
TYPE="checkbox" name="check" VALUE="cont">TOTAL CONTENT G|C|T|A<br><br>
<input type="checkbox"
name="check" value="trans">TRANSCRIPTION<br><br>
<input type="checkbox"
name="check" value="lation">TRANSLATION<br>
<p
align="center"><input type="submit"><input type="reset"></p>
</td>
</tr>
</table>
</body>
</html>
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WAMP SERVER
WAMPs are packages of independently-created programs installed on computers that use
a Microsoft Windows operating system.
WAMP is an acronym formed from the initials of the operating system Microsoft Windows
and the principal components of the package: Apache, MySQL and one of PHP, Perl or
Python. Apache is a web server. MySQL is an open-source database. PHP is a scripting
language that can manipulate information held in a database and generate web pages
dynamically each time content is requested by a browser. Other programs may also be
included in a package, such as phpMyAdmin which provides a graphical user interface for
the MySQL database manager, the alternative scripting languages Python or Perl
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RESULT
SCREEN SHOT OF PROJECT
1) LOGINSCRIPT.HTML
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2) PROJECTS.HTML
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3) SOFTWARE.HTML
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BIBLIOGRAPHY
http://www.perl.org/books/beginning-perl/
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