PROJECT REPORT CAPSTONE

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PROJECT REPORT

(Project Semester August-December 2010)

(TITLE OF THE PROJECT)

WEBDESGINING AND BIOINFORMAICS ALGORITHM---------------------------------------------

Submitted by

------------------------------------------------------------------------

(ASHISH THAKUR)

Programme & Section B.TECH BIOTECHNOLOGY (F77E3)

Under the Guidance of

----------------------------------------------------------

(Er. SREE KANTH BABU)ASSISTANT PROFESSOR

Department of Biotechnology

Lovely Institute of Engineering (LIE-F)

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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.

Er.Sree Kanth Babu

Assistant Professor

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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

Under project title WEBDESIGNING AND BIOINFORMATICS ALGORITHM. I have

used certain programming languages like PERL for algorithm writing, HTML (Hyper Text

Markup Language), CGI (Common Gateway Interface) for program connectivity. And most

important the WAMP SERVER. Its a virtual server which runs on your machine as a local

host or 127.0.0.1 in web browsers like IE, FIREFOX, and CHROME. It provides the

environment of actual server, for running the website and checking its output we use this

virtual server. We can say that its a pre-testing platform for website before going for

domain registration. My motive behind this project is to make a website which covers all

the essentials components of BIOINFORMATICS. Rather going for other sources one

should get the entire thing in one place. This is the first phase of my project next I am going

for second phase that is DATABASE development (database related to bioinformatics).

Its a live project and I get definite result of my project. It need a laptop and certainsoftware installed in it.

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INTRODUCTION TO PROGRAMMING LANGUAGE USED

HTML (Hyper Text Markup Language)

PERL (Practical Extraction and Report Language)

CGI (Common Gateway Interface)

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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.

What is a programming language?

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.

HTML (Hyper Text Markup Language)

What is HTML?

HTML is a language for describing web pages.

HTML stands forHyperText Markup Language

HTML is not a programming language, it is a markup language

A markup language is a set ofmarkup tags

HTML uses markup tags to describe web pages

HTML Tags

HTML markup tags are usually called HTML tags

HTML tags are keywords surrounded by angle brackets like

HTML tags normally come in pairs like and The first tag in a pair is the start tag, the second tag is the end tag

Start and end tags are also called opening tags and closing tags

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HTML Documents = Web Pages

HTML documents describe web pages

HTML documents contain HTML tags and plain text

HTML documents are also called 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:

My First Heading

My first paragraph.

Example Explained

The text between and describes the web page

The text between and is the visible page content

The text between and is displayed as a heading

The text between

and
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. Weuse .htm in our examples. It is a habit from the past, when the software only allowed threeletters in file extensions.

With new software it is perfectly safe to use .html.

HTML, which stands for Hyper Text Markup Language, is the predominant markup

language forweb 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 ofHTML 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 programemployed for comparing

programming languages,scripting languagesandmarkup languagesis made of 9 lines of

code in HTML, albeitNewlines are optional:

Hello HTML

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http://en.wikipedia.org/wiki/Web_pagehttp://en.wikipedia.org/wiki/Structured_documenthttp://en.wikipedia.org/wiki/Semantichttp://en.wikipedia.org/wiki/HTML_element#Images_and_objectshttp://en.wikipedia.org/wiki/HTML_element#Formshttp://en.wikipedia.org/wiki/HTML_element#Formshttp://en.wikipedia.org/wiki/HTML_elementhttp://en.wikipedia.org/wiki/Bracket#Angle_Brackets_or_Chevrons_.E2.9F.A8_.E2.9F.A9http://en.wikipedia.org/wiki/Bracket#Angle_Brackets_or_Chevrons_.E2.9F.A8_.E2.9F.A9http://en.wikipedia.org/wiki/Scripting_languagehttp://en.wikipedia.org/wiki/JavaScripthttp://en.wikipedia.org/wiki/Cascading_Style_Sheetshttp://en.wikipedia.org/wiki/W3Chttp://en.wikipedia.org/wiki/Hello_world_programhttp://en.wikipedia.org/wiki/Computer_programhttp://en.wikipedia.org/wiki/Computer_programhttp://en.wikipedia.org/wiki/Programming_languagehttp://en.wikipedia.org/wiki/Programming_languagehttp://en.wikipedia.org/wiki/Scripting_languagehttp://en.wikipedia.org/wiki/Scripting_languagehttp://en.wikipedia.org/wiki/Markup_languagehttp://en.wikipedia.org/wiki/Markup_languagehttp://en.wikipedia.org/wiki/Markup_languagehttp://en.wikipedia.org/wiki/Lines_of_codehttp://en.wikipedia.org/wiki/Lines_of_codehttp://en.wikipedia.org/wiki/Newlinehttp://en.wikipedia.org/wiki/Web_pagehttp://en.wikipedia.org/wiki/Structured_documenthttp://en.wikipedia.org/wiki/Semantichttp://en.wikipedia.org/wiki/HTML_element#Images_and_objectshttp://en.wikipedia.org/wiki/HTML_element#Formshttp://en.wikipedia.org/wiki/HTML_element#Formshttp://en.wikipedia.org/wiki/HTML_elementhttp://en.wikipedia.org/wiki/Bracket#Angle_Brackets_or_Chevrons_.E2.9F.A8_.E2.9F.A9http://en.wikipedia.org/wiki/Bracket#Angle_Brackets_or_Chevrons_.E2.9F.A8_.E2.9F.A9http://en.wikipedia.org/wiki/Scripting_languagehttp://en.wikipedia.org/wiki/JavaScripthttp://en.wikipedia.org/wiki/Cascading_Style_Sheetshttp://en.wikipedia.org/wiki/W3Chttp://en.wikipedia.org/wiki/Hello_world_programhttp://en.wikipedia.org/wiki/Computer_programhttp://en.wikipedia.org/wiki/Programming_languagehttp://en.wikipedia.org/wiki/Scripting_languagehttp://en.wikipedia.org/wiki/Markup_languagehttp://en.wikipedia.org/wiki/Lines_of_codehttp://en.wikipedia.org/wiki/Lines_of_codehttp://en.wikipedia.org/wiki/Newline


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Hello World!

BASIC WEBPAGE TEMPLATE

While most browsers will "forgive" not including the , or even the tags, leaving them out can cause problems with some browsers. For XHTML, closing tags

are absolutely required.

Your web page title here

Title tags are displayed in the top title bar of the browser.

HTML Form Tags Examples

BUTTON

EXAMPLE

Computer Experience:

Less than 1 year.

1-5 years.

More than 5 years.

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CHECKBOX

EXAMPLE


Less than 1 year.

1-5 years.

More than 5 years.

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FILE

EXAMPLE

Search your drive:

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INPUT CHECKEDHaving an input field checked by default. Can be used with Checkbox or Radio INPUT

TYPES.

EXAMPLE


Less than 1 year.

1-5 years.


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VALUE="More than 5">More than 5 years.

PASSWORD

EXAMPLE

Name?


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SIZE="20" MAXLENGTH="150">

Password?

RADIO BUTTONS

EXAMPLE

Less than 1 year.


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VALUE="1 to 5">1-5 years.

More than 5 years.

RADIO GRID

EXAMPLE

T-Shirt Order

White


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Small

Medium

Large


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MULTIPLE SUBMITEXAMPLE

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OPTION

EXAMPLE


Less than 1 year.

1-5 years.

More than 5 years.

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REDIRECT WITHOUT SUBMIT BUTTON

EXAMPLE

Select a destination:

Title Page

Sound Tags Page

Table of Contents

Text Tags Page

EXAMPLE:-2

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TEXTAREA

EXAMPLE

Tell us about your computer experience:

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PERL

(PRACTICAL EXTRACTION AND REPORT LANGUAGE)

Perl is a high-level,general-purpose, interpreted, dynamic programming language. Perl was

originally developed by Larry Wall in 1987 as a general-purpose Unix scripting language to

make report processing easier. Since then, it has undergone many changes and revisions and

become widely popular amongst programmers. Larry Wall continues to overseedevelopment of the core language, and its upcoming version, Perl 6.

The language provides powerful text processing facilities without the arbitrary data length

limits of many contemporary Unix tools, facilitating easy manipulation oftext files. It is

also used forgraphics 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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http://en.wikipedia.org/wiki/High-level_programming_languagehttp://en.wikipedia.org/wiki/List_of_programming_languages_by_categoryhttp://en.wikipedia.org/wiki/Interpreter_(computing)http://en.wikipedia.org/wiki/Dynamic_programming_languagehttp://en.wikipedia.org/wiki/Larry_Wallhttp://en.wikipedia.org/wiki/Unixhttp://en.wikipedia.org/wiki/Perl_6http://en.wikipedia.org/wiki/Text_filehttp://en.wikipedia.org/wiki/Graphicshttp://en.wikipedia.org/wiki/System_administratorhttp://en.wikipedia.org/wiki/Computer_network_programminghttp://en.wikipedia.org/wiki/Databasehttp://en.wikipedia.org/wiki/Common_Gateway_Interfacehttp://en.wikipedia.org/wiki/World_Wide_Webhttp://en.wikipedia.org/wiki/Swiss_Army_knifehttp://en.wikipedia.org/wiki/High-level_programming_languagehttp://en.wikipedia.org/wiki/List_of_programming_languages_by_categoryhttp://en.wikipedia.org/wiki/Interpreter_(computing)http://en.wikipedia.org/wiki/Dynamic_programming_languagehttp://en.wikipedia.org/wiki/Larry_Wallhttp://en.wikipedia.org/wiki/Unixhttp://en.wikipedia.org/wiki/Perl_6http://en.wikipedia.org/wiki/Text_filehttp://en.wikipedia.org/wiki/Graphicshttp://en.wikipedia.org/wiki/System_administratorhttp://en.wikipedia.org/wiki/Computer_network_programminghttp://en.wikipedia.org/wiki/Databasehttp://en.wikipedia.org/wiki/Common_Gateway_Interfacehttp://en.wikipedia.org/wiki/World_Wide_Webhttp://en.wikipedia.org/wiki/Swiss_Army_knife


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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.

To replace an occurrence oflondon by London in the string $sentence we use the

expression

$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 ofthree 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).

If we want to also replace occurrences oflOndon, lonDON, LoNDoNand so on then we

could use

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

The tr function allows character-by-character translation. The following expression

replaces each a with e, each b with d, and each c with fin the variable $sentence. The

expression returns the number of substitutions made.

$sentence =~ tr/abc/edf/

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.

$count = ($sentence =~ tr/*/*/);

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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

#!c:/perl/bin/perl # SHE BANG LINE

use CGI; # CONNECTIVITY LINE -

$cgi=new CGI; -BETWEEN PERL AND HTML

$seq=$cgi->param("seq");

@opt=$cgi->param("check");

print"content-type: text/html\n\n";

print'

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SOFTWARE #TITLE LINE REFLECT IN BROWSER

';

print'


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}

if($opt eq 'trans')

{

$seq=~ tr/atgcATGC/tacgTACG/; #TRANSCRIPTION CODE LINE

$seq=~ tr/Tt/Uu/;

print"6) TRANSCRIPTION:-$seq
";

}

if($opt eq 'lation')

{

$seq =~s/[^acgu]//ig; #TRANSLATIONTION CODE LINE

my $seq = uc($seq);

my(%genetic_code) = (

#CODON FILE

);

my ($protein) = "";

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WEB PAGE CODING

1) LOGINSCRIPT.HTML

::BIOINFO::

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CAPSTONE PROJECT

HOME|

ABOUT LPU|

PROJECTS|

CONTACT US|

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
W-

>WINDOWS
A->APACHE
M->MYSQL
P->PHP
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.
I THANK TO MY

MENTOR Er.K.SHREEKANTH BABU FOR HIS VALUABLE

GUIDANCE.

LIST OF BIOINFORMATICS DATABASES/DATABANK ONLINE

NCBI-> NATIONAL CENTER FOR BIOTECHNOLOGY

INFORMATION

EBI-> EUROPEAN

BIOINFORMATICS INSTITUTE

DDBJ-> DNA DATABANK OF

JAPAN

EMNEW-> INDEX FOR NEW EMBL NUCLEOTIDES (EBI)

PDB-> PROTEIN DATA BANK

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ExPASY-> EXPERT PROTEIN

ANALYSIS SYSTEM

PROTEIN INFORMATION

RESOURCE

OTHER LINKS

UMS LOGIN FOR INSIDE CAMPUS

UMS LOGIN FOR OUTSIDE CAMPUS

DESIGNED BY:- ASHISH THAKUR&TRADE; B.TECH-

BIOTECHNOLOGY REG.NO.->3040070009

2) PROJECTS.HTML

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PROJECT

Enter or Copy Paste

Sequence Below:-

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TOTAL NUMBER OF

NUCLEOTIDES

TOTAL CONTENT G|C|T|A

TRANSCRIPTION

TRANSLATION

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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 ofPHP, 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 asphpMyAdmin which provides a graphical user interface for

the MySQL database manager, the alternative scripting languages Python or Perl

CGI (COMMON GATEWAY INTERFACE)

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http://en.wikipedia.org/wiki/Microsoft_Windowshttp://en.wikipedia.org/wiki/Apache_HTTP_Serverhttp://en.wikipedia.org/wiki/MySQLhttp://en.wikipedia.org/wiki/PHPhttp://en.wikipedia.org/wiki/Perlhttp://en.wikipedia.org/wiki/Python_(programming_language)http://en.wikipedia.org/wiki/Web_serverhttp://en.wikipedia.org/wiki/PhpMyAdminhttp://en.wikipedia.org/wiki/Microsoft_Windowshttp://en.wikipedia.org/wiki/Apache_HTTP_Serverhttp://en.wikipedia.org/wiki/MySQLhttp://en.wikipedia.org/wiki/PHPhttp://en.wikipedia.org/wiki/Perlhttp://en.wikipedia.org/wiki/Python_(programming_language)http://en.wikipedia.org/wiki/Web_serverhttp://en.wikipedia.org/wiki/PhpMyAdmin


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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

For WAMP information:-

http://www.tagbytag.org/tutorials/getting-started/web-design-

software/wamp-guide

For HTML information:-

http://www.quackit.com/html/tutorial/

http://www.w3schools.com/html/html_primary.asp

http://www.echoecho.com/htmlbasics01.htm

For PERL information:-

Learning Perl (4th edition)

Randal SchwartzandTom Phoenixandbrian d foy

Release date 01 Jul 2005

Publisher O'Reilly & Associates

ISBN 0-596-10105-8

http://www.perl.org/books/beginning-perl/

FOR CGI information:-

http://blob.perl.org/books/beginning-perl/3145_Chap12.pdf
http://www.tagbytag.org/tutorials/getting-started/web-design-software/wamp-guidehttp://www.tagbytag.org/tutorials/getting-started/web-design-software/wamp-guidehttp://www.quackit.com/html/tutorial/http://www.w3schools.com/html/html_primary.asphttp://www.echoecho.com/htmlbasics01.htmhttp://books.perl.org/author/56http://books.perl.org/author/82http://books.perl.org/publisher/orashttp://www.perl.org/books/beginning-perl/http://blob.perl.org/books/beginning-perl/3145_Chap12.pdfhttp://www.tagbytag.org/tutorials/getting-started/web-design-software/wamp-guidehttp://www.tagbytag.org/tutorials/getting-started/web-design-software/wamp-guidehttp://www.quackit.com/html/tutorial/http://www.w3schools.com/html/html_primary.asphttp://www.echoecho.com/htmlbasics01.htmhttp://books.perl.org/author/56http://books.perl.org/author/82http://books.perl.org/publisher/orashttp://www.perl.org/books/beginning-perl/http://blob.perl.org/books/beginning-perl/3145_Chap12.pdf

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