You are on page 1of 59

BIO SEQUENCE ANALYSER Page | 1

1. INTRODUCTION

The project entitled “BIO SEQUENCE ANALYSER”. It is based on Bioinformatics


using data mining. Bioinformatics is an interdisciplinary field that develops methods and
software tools for understanding biological data. Bio Sequence Analyser provides the facility
for analyses DNA, RNA and Protein Sequences. It is an essential tool, which helps in
biological researches.
The introduction of new technologies leads to an exponential growth of collected data
in many areas. Traditional data analysis techniques often fail to process large amounts of data
efficiently. In this case data mining technology can be used to extract knowledge from large
amount of data. Recently, the collection of biological data like protein sequences, DNA
sequences etc. is increasing at explosive rate due to improvements of existing technologies
and the introduction of new ones such as the microarrays. Traditional data analysis
techniques are unable to extract meaningful information from the huge amount of biological
data sequences, such as the DNA, RNA, protein etc. One important area of research is to
classify protein sequences into different families, classes or sub classes. One of the emerging
techniques for handling such sequences is data mining. classification is the most important
technique to identify a particular character or a group of them.
Different classification methods or algorithms have been proposed by different
researchers to classify the protein sequences. The Protein sequence consists of twenty
different amino acids which are arranged in some specific sequences. Popular protein
sequence classification techniques involve extraction of specific features from the sequences.
These features depend on the structural and functional properties of amino acids. These
features are compared with their predefined values. Researchers apply some well-known
classification techniques like neural networks, Genetic algorithm, Fuzzy ARTMAP, Rough
Set Classifier etc. Till date, none have achieved 100% accuracy level.
A very important issue in bioinformatics is data mining in biological databases. Large
databases were created for the recording and exploitation of biological data, due to the human
DNA and protein decoding. In fact, over 20 trillion basic structural DNA elements are
recorded in the three large biological databases at that moment.

UNIVERSITY INSTITUTE OF TECHNOLOGY, Kollam 2017


BIO SEQUENCE ANALYSER Page | 2

2. ORGANIZATIONAL PROFILE
Technology Centre for Software and Research (TCSR) is a dynamic group of highly
competent IT professionals providing cost effective and cutting-edge IT solutions with
integration of Data Mining/Research tools and Applications. Their focus is greater return for
their client‟s technology investment. They are a dynamic company where teamwork and
common goals are the main driving force. Expert and timely delivery of customized solutions
is what they can do best.
Technology Centre for Software and Research (TCSR) is a professional web design
company, offering first-class website development services, Internet Marketing and
Promotion, E-Commerce and Content Management solutions to clients. Their services
include new domain name search and registration, site design and development (including
photography, graphics, and writing), and ongoing maintenance of your sites.
 Custom Design & Layout
 Custom HTML Programming
 Custom Graphic Design (GUI)
 Professional Digital Photography
 Library of Over thousands of Professional Web Templates
 Available JavaScript, Java, Perl, ASP, .Net, VC++, PHP, VB Programming
 Flash & Shockwave Programming Technology
 Online Forms & E-mail
 Search Engine Optimization (SEO)
 Custom Web Site Performance Statistics
 Business Analytics
Company‟s Mission Statement
Technology Centre for Software and Research (TCSR) powering is innovative, cost-
effective and quality solutions in Web applications, Intelligent Systems and Software
Applications.

UNIVERSITY INSTITUTE OF TECHNOLOGY, Kollam 2017


BIO SEQUENCE ANALYSER Page | 3

3. SYSTEM ANALYSIS AND DESIGN

System analysis is a logical process; the objective of this phase is not actually to solve
the problem but to determine what must be done to solve the problem. The basic objective of
the analysis stage is to develop the logical model of the system using tools such as the data
flow diagram and elementary data description of the elementary algorithm. The logical model
is Subject to review by both the management and the user who agree that the model does in
fact reflect what should be done to solve the problem.
System analysis is not a precise science. It is in fact more of an art, aided by scientific
approach to find definition and recording data, gathering traditional structures is only one part
of the system analysis, the next step is to examine the data, assess the situation and looking at
the alternatives.

3.1 EXISTING SYSTEM


Currently, a lot of bioinformatics work is concerned with the technology of databases.
The available bioinformatics databases are specific to certain proteins and not deal with data
in different sources. For example, a Nucleotide database typically contains information about
Nucleotide not about RNA or DNA. The available databases are used for only certain specific
function only. The difficulty of learning each individual tools and integrating various tools
and databases arises the need for a platform independent environment for multiple biological
data access and analysis.
The main drawbacks of Existing Systems are;
 There is no common database for DNA, RNA, and Nucleotide etc.
 The private databases those used by research groups are not accessible by user
 The data in some databases are static in nature
 Most database are structural database
 The user require more domain knowledge to access the data

3.2 PROPOSED SYSTEM


The “Bio Sequence Analyser” can store the protein sequence of different organisms.
The researchers can access the sequence information and use the information for various
research operations. The user can access the latest findings of the researchers through the
system. The system provides a platform for user to learn the Bioinformatics field. The
system enables the connected computers with the aid of his user name and password. The
system enables the researcher access different protein sequence of different organism for their
work and generates queries in different format.
Advantages of Proposed System are;

UNIVERSITY INSTITUTE OF TECHNOLOGY, Kollam 2017


BIO SEQUENCE ANALYSER Page | 4

 Provide various similarity measurement tool


 The user can access the latest findings of various Researchers
 The user can not require more domain knowledge of Bioinformatics
 Provides platform for doing various sequence mining operations
 It helps the Biological Researchers to find out various Research Guides.
 Provides Facility to store DNA, RNA, and protein Sequences
 Analyses these Genetical information‟s
 Check the similarity of these Sequence
 To extract the features of the Sequence
 To keep the researcher and guide relationship
 The Guide can assign jobs to the researcher
 The Researcher and Guide can upload tutorials for common users

3.3 FEASIBILITY STUDY


The main objective of the feasibility study is to treat the technical, operational, logical
and economic feasibility of developing the computerized system. All systems are feasible,
given unlimited resources and infinite time. It is both necessary and prudent to evaluate the
feasibility of the project at System study phase itself. The feasibility study to be conducted
for this project involves.

1. Technical Feasibility

2. Operational Feasibility

3. Economic Feasibility

3.3.1 Technical Feasibility

Technical feasibility includes Risk Resources availability and technologies. The


management provides latest hardware and software facilities for the successful completion of
the projects. With these latest hardware and software support the system will perform
extremely well. The system is available through Internet.
3.3.2 Operational Feasibility

In the existing system it is very difficult to maintain and update huge amount of
information. The development of the system was started because of the requirement put
forward by the management. This system, will handles the request in a better way and make
the process easier thus, it is sure that the system developed is operationally feasible.

UNIVERSITY INSTITUTE OF TECHNOLOGY, Kollam 2017


BIO SEQUENCE ANALYSER Page | 5

3.3.3 Economic Feasibility

In the economic feasibility the development cost of the system is evaluated weighing
it against the ultimate benefit derived from the new system. It is found that the benefit, from
the new system would be more than the cost and time involved in its development.

3.4 SYSTEM SPECIFICATION

3.4.1 Software Specification


Operating System : Windows Operating System

Web Server : Apache Tomcat

Web Browser : Internet Explorer/Mozilla/Chrome

Front-End Tool : PHP

Client side Script : JavaScript

Server side Script : PHP

Back-End Tool : MySQL

3.4.2 Hardware Specification

Processor : x386/32-bit

RAM : 128 MB or Higher

Hard Disk : 40 GB or higher

3.5 SOFTWARE TECHNOLOGY REVIEW

3.5.1 Overview of PHP (PHP-5.0):


PHP is a widely-used Open Source general-purpose scripting language that is
especially suited for Web applications and can be embedded into HTML. It is a free software.
Its syntax draws upon C, Java, and Perl, and is easy to learn. The main goal of the language is
to allow web developers to write dynamically generated web pages quickly. One of the most
important factors driving PHP‟s popularity over the last couple of years has been its support
for a variety of databases, including MySQL, Oracle, and Microsoft Access. One of the most
powerful combinations in the open source arena today is the PHP/ MySQL combination. Like
PHP, MySQL has open-source roots: it is a fast and reliable database management system
that is rapidly acquiring a worldwide user base. By using PHP and MySQL together, users
can benefit from the cost savings that accompany community-driven software, and also

UNIVERSITY INSTITUTE OF TECHNOLOGY, Kollam 2017


BIO SEQUENCE ANALYSER Page | 6

leverage off the immense number of freely available PHP/MySQL applications to reduce
development time.
Typically, PHP code is embedded inside a regular HTML document, and is
recognized and executed by the web server when the document is requested through a
browser. Because PHP is a full-featured programming language, you can code all manner of
complex thin gummies into your web pages using this technique; the server will execute your
code and return the output to the browser in the format you specify. Because PHP code is
executed on the server and not on the client, developers don‟t have to worry about browser-
specific quirks that could cause the code to break (as commonly happens with JavaScript);
PHP code works independently of the user‟s web browser.
Advantages of PHP

1 Vs. Pure Servlets - It is more convenient to write (and to modify) regular HTML than
to have a zillion print statements that generate the HTML.
2 Vs. Server-Side - Includes (SSI).SSI is a widely support technology for including
externally defined pieces into a static web page.
3 Vs. JavaScript - JavaScript can generate HTML dynamically on the client. This is the
useful capability, but only handles situations where the dynamic information is based
on the client‟s environment. With the exception of cookies, HTTP and form
submission data is not available to JavaScript. And, since it runs on the client,
JavaScript can‟t access server-side resources like databases, catalogs, pricing
information, and the like.
4 Vs. Static HTML - Regular HTML, of course, cannot contain dynamic information.
PHP is so easy and convenient that it is quite feasible to augment HTML pages that
only benefit marginally by the insertion of small amounts of dynamic data.
Previously, the cost of using dynamic data would preclude its use in all but the most
valuable instances.

Syntax and Semantics


PHP only parses code within its delimiters. Anything outside its delimiters is sent
directly to the output and is not parsed by PHP. The most common delimiters
are <?php and ?>, which known as open and close delimiters respectively in the PHP
language. <script language="php"> and </script> delimiters are also available. Short tags can be
used to start PHP code, <? or <?= (which is used to echo back a string or variable) and the tag
to end PHP code, ?>.

3.5.2 HTML (Hyper Text Markup Language)


Hypertext Markup Language (HTML), the languages of the World Wide Web
(WWW), allows users to produces Web pages that include text, graphics and pointer to other
Web pages (Hyperlinks).

UNIVERSITY INSTITUTE OF TECHNOLOGY, Kollam 2017


BIO SEQUENCE ANALYSER Page | 7

HTML is not a programming language but it is an application of ISO Standard 8879,


SGML (Standard Generalized Markup Language), but specialized to hypertext and adapted to
the Web. The idea behind Hypertext is that instead of reading text in rigid linear structure, we
can easily jump from one point to another point. We can navigate through the information
based on our interest and preference. A markup language is simply a series of elements, each
delimited with special characters that define how text or other items enclosed within the
elements should be displayed. Hyperlinks are underlined or emphasized works that load to
other documents or some portions of the same document.

Advantages:
 A HTML document is small and hence easy to send over the net. It is small because it
does not include formatted information.

 HTML is platform independent.

 HTML tags are not case-sensitive.

3.5.3 JavaScript:
JavaScript is a script-based programming language that was developed by Netscape
Communication Corporation. JavaScript was originally called Live Script and renamed as
JavaScript to indicate its relationship with Java. JavaScript supports the development of both
client and server components of Web-based applications. On the client side, it can be used to
write programs that are executed by a Web browser within the context of a Web page. On the
server side, it can be used to write Web server programs that can process information
submitted by a Web browser and then updates the browser‟s display accordingly.
Even though JavaScript supports both client and server Web programming, we prefer
JavaScript at Client side programming since most of the browsers supports it. JavaScript is
almost as easy to learn as HTML, and JavaScript statements can be included in HTML
documents by enclosing the statements between a pair of scripting tags,
<SCRIPTS>.. </SCRIPT>.
<SCRIPT LANGUAGE = “JavaScript”>
JavaScript statements
</SCRIPT>

3.5.4 MySQL
MySQL is an open source, SQL Relational Database Management System (RDBMS)
that is free for many uses (more detail on that later). Early in its history, MySQL occasionally
faced opposition due to its lack of support for some core SQL constructs such as sub selects
and foreign keys. Ultimately, however, MySQL found a broad, enthusiastic user base for its

UNIVERSITY INSTITUTE OF TECHNOLOGY, Kollam 2017


BIO SEQUENCE ANALYSER Page | 8

liberal licensing terms, perky performance, and ease of use. Its acceptance was aided in part
by the wide variety of other technologies such as PHP, Java, Perl, Python, and the like that
have encouraged its use through stable, well-documented modules and extensions. MySQL
has not failed to reward the loyalty of these users with the addition of both sub selects and
foreign keys as of the 4.1 series. Like many competing products, both free and commercial,
MySQL isn‟t a database until you give it some structure and form.

Features
MySQL‟s development history has always been characterized by a clear-eyed focus
on the most important attributes of a good RDBMS: speed and stability. This has resulted in a
system that outperforms most of its competitors without sacrificing reliability or ease of use,
thereby gaining it a loyal base of developers, administrators, and users worldwide.
The following sections describe MySQL‟s most compelling features.

Speed: In an RDBMS, speed—the time taken to execute a query and return the results to the
caller—is everything. MySQL scores high on this parameter, with better performance than
almost all its competitors.

Reliability: When it comes to reliability, MySQL‟s creeds are impeccable. The MySQL
RDBMS has been tested and certified for use in high-volume, mission-critical applications by
some of the world‟s largest organizations, including NASA, HP, and Yahoo! Because
MySQL has deep roots in the open-source community, every new release is typically “battle-
tested” by users all over the world, on different operating systems and in different operating
conditions, to ensure that it is reliable in all conditions.

Security: Security is an important concern when dealing with multi-user databases, and
MySQL‟s developers have taken a great deal of care to ensure that MySQL is as secure as
possible. MySQL comes with a sophisticated access control and privilege system to prevent
unauthorized users from accessing the system. This system, implemented as a five-tiered
privilege hierarchy, enables MySQL administrators to protect access to sensitive data using a
combination of user- and host-based authentication schemes. Users can be restricted to
performing operations only on specified databases or fields, and MySQL even makes it
possible to control which types of queries a user can run, at database, table, or field level.

Scalability and Portability: MySQL can handle extremely large and complex databases
without too much of a drop in performance. Tables of several gigabytes containing hundreds
of thousands of records are not uncommon, and the MySQL web site itself claims to use
databases containing 50 million records. And once you‟ve got your tables filled with data,
you can move them from one platform to another without any difficulty—MySQL is
available for both UNIX and non-UNIX operating systems, including Linux, Solaris,
FreeBSD, OS/2, MacOS, and Windows 95, 98, Me, 2000, XP, and NT. We can conclude as,

UNIVERSITY INSTITUTE OF TECHNOLOGY, Kollam 2017


BIO SEQUENCE ANALYSER Page | 9

 MySQL was found to have the best performance and scalability, along with Oracle 9i,
of the systems under comparison.
 MySQL was the easiest RDBMS to tune and optimize, along with SQL Server, of the
systems under comparison.
 MySQL scaled efficiently at loads from 50 to 1,000 simultaneous users, with
performance dropping only marginally once the 600-user limit had been crossed.
 MySQL code quality was found to rank higher than comparable commercial software,
with a defect density six times lower.

 MySQL‟s development team was extremely responsive to defect reports, resolving


them rapidly and efficiently.

3.6 DATA FLOW DIAGRAM

Data Flow Diagram (DFD) representing a system at any level of detail with a graphic
network of symbols showing data flows, data stores, data processes, and data sources. The
purpose of DFD is to provide a semantic bridge between users and system developers. The
diagram is the basis of structured system analysis.
A level 0 DFD, also called a fundamental system model or a context model represents
the entire software elements as a single bubble with input and output indicated by incoming
and outgoing arrows respectively. Additional process and information flow parts are
represented in the next level i.e., Level 1 DFD. Each of the processes represented at Level 1
are sub functions of overall system depicted in the context model. Any processes, which are
complex in Level 1, will be further represented into sub functions in the next level, i.e., in
level 2.
Data flow diagrams illustrate how data is processed by a system in terms of inputs,
and outputs. Represent major components or functions with Circles. Actions for input by a
user or a system go in Rectangular Boxes. Databases are represented by Parallel lines
enclosing a phrase corner.

3.6.1 Data Flow Diagram – The Rules

1. External Entities
External entities are objects outside the system, with which the system communicates.
External entities are sources and destinations of the system‟s inputs and outputs.
2. Processes
When naming processes, avoid glossing over them, without really understanding their
role. Indications that this has been done are the use of vague terms in the descriptive title area
like „process‟ or „update‟. The most important thing is that the description must be
meaningful to whoever will be using the diagram.
3. Data Flows

UNIVERSITY INSTITUTE OF TECHNOLOGY, Kollam 2017


BIO SEQUENCE ANALYSER Page | 10

Double-headed arrows can be used (to show two-way flows) on all but bottom level
diagrams. Furthermore, in common with most of the other symbols used, a data flow at a
particular level of a diagram may be decomposed to multiple data flows at lower levels.
4. Data Store
Data store represent stores of data within the systems and are represented by open
rectangle. Data Flows represent the movements of data between other components and are
shown by arrows.

Rectangular box defined a source of destination of the system

A circle stands for processes that convert data into information

Data Flow

A Parallel line is a data store

Level 0 : Context Diagram

UNIVERSITY INSTITUTE OF TECHNOLOGY, Kollam 2017


BIO SEQUENCE ANALYSER Page | 11

Level 1 : Admin

UNIVERSITY INSTITUTE OF TECHNOLOGY, Kollam 2017


BIO SEQUENCE ANALYSER Page | 12

Level 1: Researcher

UNIVERSITY INSTITUTE OF TECHNOLOGY, Kollam 2017


BIO SEQUENCE ANALYSER Page | 13

Level 1: Researcher Guide

UNIVERSITY INSTITUTE OF TECHNOLOGY, Kollam 2017


BIO SEQUENCE ANALYSER Page | 14

Level 1: Common User

UNIVERSITY INSTITUTE OF TECHNOLOGY, Kollam 2017


BIO SEQUENCE ANALYSER Page | 15

Level 2: Analysis of Researcher

Level 2: Job of Researcher Guide

UNIVERSITY INSTITUTE OF TECHNOLOGY, Kollam 2017


BIO SEQUENCE ANALYSER Page | 16

3.7 STRUCTURE CHART

UNIVERSITY INSTITUTE OF TECHNOLOGY, Kollam 2017


BIO SEQUENCE ANALYSER Page | 17

UNIVERSITY INSTITUTE OF TECHNOLOGY, Kollam 2017


BIO SEQUENCE ANALYSER Page | 18

3.8 MENU TREE

UNIVERSITY INSTITUTE OF TECHNOLOGY, Kollam 2017


BIO SEQUENCE ANALYSER Page | 19

UNIVERSITY INSTITUTE OF TECHNOLOGY, Kollam 2017


BIO SEQUENCE ANALYSER Page | 20

3.9 SYSTEM FLOW CHART

UNIVERSITY INSTITUTE OF TECHNOLOGY, Kollam 2017


BIO SEQUENCE ANALYSER Page | 21

4. SYSTEM DESIGN

System design involves translating information requirements and conceptual design


into technical specification and general flow of processing. After the project idea is specified,
related information is gathered and a way to evolve the system is developed. The process
starts with a study of the outputs required of the system, the inputs given, the data that is to be
stored, how to store the data, the data structured for storage.

4.1 MODULE DESCRIPTION

The System is divided into three modules namely admin, researcher and user. Each
module specifies the functional requirement of the system.
4.1.1 Admin Module

The administrator do overall control of the system. If your user name and password is
matching with administrator‟s user id and password, then you will enter in to the site as
administrator. You will access the functions of administrator from this page. The
functionality of admin module is;
 User control
 Generate Reports
 Add, Remove or Update Tutorial
 Add or update Sequence
 Similarity Analysis
 Feature Extraction
 View profiles of Researcher and Research Guide
4.1.2 Common User Module

The common user is the one who uses the site. The common users such as biological
students or other persons can perform :
 View Tutorials
 Check Similarity of DNA,RNA, and Protein Sequence
 View features of DNA,RNA and Protein Sequences
 DNA to Protein Conversion
4.1.3 Researcher Module

The researcher module can be used to provide a platform for performing various
biological sequence operations. The authenticated researcher can access the site with their
user name and password. The main functions of researcher module are described below:

UNIVERSITY INSTITUTE OF TECHNOLOGY, Kollam 2017


BIO SEQUENCE ANALYSER Page | 22

 Add DNA,RNA, and Protein sequences


 Features extraction
 Similarity Analysis
 DNA to Protein
 View Jobs
 Upload tutorials
 Update profile

4.1.4 Research Guide Module

The Research Guide module can be used to provide a platform for support the
researchers and performing various biological sequence operations. The authenticated
Research Guide can access the site with their user name and password. The main functions of
Research Guide module are described below:
 Assign Job to Researcher
 Check Job Status
 Features extraction
 Similarity Analysis
 Graphical Reports
 Upload tutorials
 Update profile

4.2 INPUT DESIGN

Input design is the method by which valid data are accepted from the user. This part
of the designing requires very careful attention. If the data going into the system is incorrect
then the processing and output will magnify these errors. Inaccurate input data are the most
common cause of errors in data processing. Input design consists of the following processes:-
 Designing graphical user entry screen is easy to use.
 Designing procedures and functions to valid the data as per business rules.
 Designing functions needed to store data into a usable form for processing.
 Designing the common integrated functions that can be used by all other users when
needed.
4.2.1 Input Objectives
 Controlling Amount of Input: Wherever user input is required, giving possible input
values as default in that area reduces the amount of user keystrokes. Thus the user can
pass on to next data without much typing. This makes the data entry much fast and

UNIVERSITY INSTITUTE OF TECHNOLOGY, Kollam 2017


BIO SEQUENCE ANALYSER Page | 23

error free. When the user has the format of input to be given, it will be very easy for
the user to give input in the same format.

 Avoiding Delay: A processing delay resulting from data entry operations is called a
bottleneck. Such bottlenecks are made obsolete in this project by breaking up the
amount of data to be entered in each form into different smaller and simpler forms.

 Avoiding Errors in Data: The rate at which errors occur depends on the quantity of
the data. As told in the above objective these errors are reduced by making the
number of data to be entered in each form is reduced.

 Avoiding Extra Steps: To fulfill any operation the user have no need to do complex
steps, instead any operation can be done with simple easy to use steps.

Login Form:

UNIVERSITY INSTITUTE OF TECHNOLOGY, Kollam 2017


BIO SEQUENCE ANALYSER Page | 24

Research Guide Registration Form:

Researcher Registration Form:

UNIVERSITY INSTITUTE OF TECHNOLOGY, Kollam 2017


BIO SEQUENCE ANALYSER Page | 25

Form for Assign Job:

Form for Add Sequence:

UNIVERSITY INSTITUTE OF TECHNOLOGY, Kollam 2017


BIO SEQUENCE ANALYSER Page | 26

Form for Similarity Analysis:

4.3 OUTPUT DESIGN


Output design is one of the most important features of the information system. When
the output is not of good quality, the users will be averse to use the newly designed system
and may not use the system. There are many types of outputs, all of which can be either
highly useful or can be critical to the users, depending on the manner and degree to which
they are used.
Outputs from computer system are required primarily to communicate the results of
processing to users. They are also used to provide a permanent hard copy of the results for
later consultation.
4.3.1 Output Objectives
The output from an information system should accomplish one or more of the
following objectives:

 Convey information about past activities, current status, or projections of the future.
 Signal important events, opportunities, problems or warnings
 Trigger an action
 Confirm an action

4.4 ANALYSIS TOOLS


System analysis is the process of collecting and interpreting facts, understanding
problems and using the information to suggest improvements on the system. This will help to

UNIVERSITY INSTITUTE OF TECHNOLOGY, Kollam 2017


BIO SEQUENCE ANALYSER Page | 27

understand the existing system and determine how computers make its operation more
effective.
4.5 Database Design
The database design is a logical development in the methods used by the computers to
access and manipulate data stored in the various parts of the computer systems. Database is
defined as an integrated collection of data. The overall objective in the development of
database technology has been to treat data as an organizational resource and as an integrated
whole. The main objectives of databases are data integrity and data independence.
A database is a collection of interrelated data stored with minimum redundancy to
serve many users quickly and effectively. The database serves as the repository of data, so a
well-designed database can lead to a better program structure and reduce procedural
complexity. In a database environment, common data are available and used by several users
Database Management System (DBMS) allow the data to be protected and organized
separately from other resources like hardware, software, and programs. DBMS is a software
package, which contains components that are not found other data management packages.
The significant of DBMS is the separation of data as seen by the programs and data as stored
on the direct access storage devices. That is the difference between the logical and physical
data.
The main objectives covered in database design are:
 Controlled redundancy
 Data independence
 Accuracy and integrity
 Privacy and security
 Performance

The database tables used in this project are given below

Table List

Sl. No Table Name Description

1 Login It contains Login details of Admin,


Researcher and Researcher guide
2 Researcher Reg Researcher Registration details

3 Guide Reg Research Guide Registration details

4 Job Researcher Job details

5 Content Details of Sequences such as DNA, RNA


and Protein

UNIVERSITY INSTITUTE OF TECHNOLOGY, Kollam 2017


BIO SEQUENCE ANALYSER Page | 28

6 Features Features of DNA, RNA and Protein

7 Tutorial Information Related to Tutorial

8 Message Communication between researcher and


Guide
9 Similarity Similarity Analysis details

10 Research Paper Information related to research paper

1. LOGIN
Name Type Length Constraints Description
User id Varchar 15 Primary key User id
Not null
Pwd Varchar 15 Not null Password
Type Varchar 15 Not null Type of the user
Status Int Not null Status of the user

2. RESEARCHER REG
Name Type Length Constraints Description
R ID Varchar 15 Primary key Registration id of the
Not null researcher
Name Varchar 20 Not null Name of the user
Gen Varchar 7 Not null Gender
DOB Date Date of birth
Mob Int Not null Mobile number
Location Varchar 30 Location
Email Varchar 20 Not null Email id of the user
Qtn Varchar 20 Not null Qualification
Rarea Varchar 25 not null Research area

3. Job
Name Type Length Constraints Description
Job id Varchar 15 Primary key Job id
Not null
Title Varchar 20 Not null Job title
Adate Date Not null Job assigning date
Cdate Date Not null Job completing date
Status Varchar 10 Not null Job status
(Pending/completed)

4. Content
Name Type Length Constraints Description
Type Varchar 10 Not null Type of the
content(Protein/DNA/RNA)

UNIVERSITY INSTITUTE OF TECHNOLOGY, Kollam 2017


BIO SEQUENCE ANALYSER Page | 29

Seq id Varchar 15 Primary key Sequence id


Not null
Seq Varchar 1000 Not null Sequence
F id Varchar 15 Not null Feature id

5. Features
Name Type Length Constraints Description
F id Varchar 15 Primary key Feature id
Not null
F name Varchar 20 Not null Feature name
Fts Varchar 50 Not null Features

6. Tutorial
Name Type Length Constraints Description
T id Varchar 15 Primary key Tutorial id
Not null
Title Varchar 20 Not null Title
Udate Date Not null Upload date
Vcount Int Not null Visitors number

7. Guide Reg
Name Type Length Constraints Description
G ID Varchar 15 Primary key Registration id of the
Not null research guide
Name Varchar 20 Not null Name of the user
Gen Varchar 7 Not null Gender
DOB Date Date of birth
Mob Int 15 Not null Mobile number
Location Varchar 30 Location
Email Varchar 20 Not null Email id of the user
Qtn Varchar 20 Not null Qualification
Spcl Varchar 25 not null Specialization
Dgnt Varchar 20 Not null Designation

8. Message
Name Type Length Constraints Description
M id Varchar 15 Primary key Message id
Not null (generated from To and
From)
To Varchar 20 Not null Message receiver
From Varchar 20 Not null Message sender
Subject Varchar 20 Subject of the message
Content Varchar 200 Not null Content of the message
Status Int Not null Status of the message

9. Similarity
Name Type Length Constraints Description

UNIVERSITY INSTITUTE OF TECHNOLOGY, Kollam 2017


BIO SEQUENCE ANALYSER Page | 30

Pid1 Varchar 25 Not null Protein id 1


Pid2 Varchar 25 Not null Protein id 2
Sst Int Not null Similarity state
Cdate Date Not null Check date

10. Research Paper


Name Type Length Constraints Description
P id Varchar 15 Primary key Paper ID
Not null
Atr1 Varchar 20 Not null Author 1
Atr2 Varchar 20 Author 2
DOP Date Not null Date of publish
Jn Varchar 25 Not null Journal name

UNIVERSITY INSTITUTE OF TECHNOLOGY, Kollam 2017


BIO SEQUENCE ANALYSER Page | 31

5. SYSTEM CODING
5.1 PROGRAM LIST

Program Name Description


Home.html Home page of Bio Sequence Analyser
Login.php Login page
Reghome.php Registration home
Researcher_reg.php Researcher registration
Guide_reg.php Research Guide registration
Tutor.php Tutorial
Contact.php Contact
researcherhome.php Researcher home page
addsequence.php Page for Add Sequence
FeaturesExtraction.php Page for Feature Extraction
jobstatus.php Page for check job status
SimilarityAnalysisHome.php Page for similarity analysis
DNAtoProtein.php Page for DNA to Protein Conversion
UploadTutorial.php Upload tutorial
Adminhome.php Admin home page
assignjob.php Page for assign job
featuresview.php Page for view Sequence features
Report.php Page for Generate Report
Msg.php Communication window
DNA_Analysis.php DNA Analysis
RNA_Analysis.php RNA Analysis
Protein_Analysis.php Protein Analysis
Reserch_paper.php Research Papers
Feedback.php Feedback form
User_control.php Control Researcher and Guide Users
Profile.php Check Profiles of Users
Seq_Controll.php Add/ Update Sequences
Researcherlist.php Researcher‟s List

UNIVERSITY INSTITUTE OF TECHNOLOGY, Kollam 2017


BIO SEQUENCE ANALYSER Page | 32

5.2 SOURCE CODE

Home.html
<!DOCTYPE html>
<!--[if IE 8 ]><html class="no-js oldie ie8" lang="en"> <![endif]-->
<!--[if IE 9 ]><html class="no-js oldie ie9" lang="en"> <![endif]-->
<!--[if (gte IE 9)|!(IE)]><!--><html class="no-js" lang="en"> <!--<![endif]-->
<head>
<meta charset="utf-8">
<title>TechBio- Bio Sequence Analyser</title>
<meta name="description" content="">
<meta name="author" content="">
<meta name="viewport" content="width=device-width, initial-scale=1, maximum-
scale=1">
<link rel="stylesheet" href="css/base.css">
<link rel="stylesheet" href="css/vendor.min.css">
<link rel="stylesheet" href="css/main.css">
<script src="js/modernizr.js"></script>
<link rel="shortcut icon" href="favicon.png" >
</head>
<body>
<header id="main-header">
<div class="row">
<nav id="nav-wrap">
<a class="mobile-btn" href="#nav-wrap" title="Show navigation">
<span class="menu-icon">Menu</span>
</a>
<a class="mobile-btn" href="#" title="Hide navigation">
<span class="menu-icon">Menu</span>
</a>
<ul id="nav" class="nav">

UNIVERSITY INSTITUTE OF TECHNOLOGY, Kollam 2017


BIO SEQUENCE ANALYSER Page | 33

<li><a class="smoothscroll" href="home.html">Home.</a></li>


<li><a href="tutorial.php">Tutorial</a></li>
<li><a href="Reghome.php">Registration</a></li>
<li><a href="login.php">Login</a></li>
<li><a href="contact.php">Contact.</a></li>
</ul> <!-- end #nav -->
</nav> <!-- end #nav-wrap -->
</div>
</header> <!-- end header -->
<section id="hero">
<div class="row hero-content">
<div class="twelve columns hero-container">
<div id="hero-slider" class="flexslider">
<ul class="slides">
<li>
<div class="flex-caption">
<h1 class=""><img src="images/portfolio/Logobio123.png" alt="Underwater">
<h1 class="">Say hello to <span>Tech-Bio</span>.We present an integrated tool for
preprocessing and analysis of genetic data.
</h1>
<h3 class="">Tech-Bio is a BioSequence Analyser, which is based on Bioinformatics
using data mining.</h3>
</div></li><li>
<div class="flex-caption">
<h1 class="">We provides the facility for analyses DNA, RNA and Protein
Sequences.</h1>
<h3 class="">Tech-Bio is a BioSequence Analyser, which is based on Bioinformatics
using data mining.</h3>
</div></li><li>
<div class="flex-caption">
<h1 class="">We helps biological researches for preprocessing and analysis of genetic
data.</h1>

UNIVERSITY INSTITUTE OF TECHNOLOGY, Kollam 2017


BIO SEQUENCE ANALYSER Page | 34

<h3 class="">Tech-Bio is a BioSequence Analyser, which is based on Bioinformatics


using data mining.</h3></div></li>
</ul></div></div>
</div>
</section>
<div id="preloader">
<div id="loader"></div>
</div>
<script src="js/jquery-1.11.3.min.js"></script>
<script src="js/jquery-migrate-1.2.1.min.js"></script>
<script src="js/jquery.flexslider-min.js"></script>
<script src="js/jquery.waypoints.min.js"></script>
<script src="js/jquery.validate.min.js"></script>
<script src="js/jquery.fittext.js"></script>
<script src="js/jquery.placeholder.min.js"></script>
<script src="js/jquery.magnific-popup.min.js"></script>
<script src="js/main.js"></script>
</body>
</html>

Login.php
<html>
<title>Registration</title>
<head>
<script language="javascript" type="text/javascript">
function checkform()
{
if (document.login.user.value=="")
{
alert('PLEASE ENTER THE USER NAME ');
document.login.user.focus();
return false;

UNIVERSITY INSTITUTE OF TECHNOLOGY, Kollam 2017


BIO SEQUENCE ANALYSER Page | 35

}
else if (document.login.pass.value=="")
{
// something is wrong
alert('PLEASE ENTER THE PASSWORD');
document.login.pass.focus();
return false;
}
}
</script>
</head>
<body>
<center><br>
<h2>LOGIN</h2>
<form action="#" method=post name="login" onSubmit="return checkform()">
<pre>
User Name : <input type=text name=user placeholder="User Name">
Password : <input type=password name=pass placeholder="Password">
<input type=submit name=Submit>
</body>
</html>
<?php
if(isset($_POST["Submit"]))
{
$user=$_POST['user'];
$pass=$_POST['pass'];
$count1=0; $count2=0;
$count1=substr_count($user, "'");
$count2=substr_count($pass, "'");
$err=0;
if ($count1>0 || $count2>0)
$err=1;

UNIVERSITY INSTITUTE OF TECHNOLOGY, Kollam 2017


BIO SEQUENCE ANALYSER Page | 36

$conn=mysql_connect("localhost","root","");
if (!$conn)
{
die('Could not connect: ' . mysql_error());
}
mysql_select_db("techbio",$conn);
$sql="select user_id,pwd from login where user_id='$user'";
mysql_query($sql);
$result = mysql_query("SELECT * from login where user_id='".$user."' and
pwd='".$pass."'");
$flag=0;
$type=null;
if($row = mysql_fetch_array($result))
{
$flag=1;
$type=$row['type'];
session_start();
$_SESSION['type'] = $type; // store session data
$_SESSION['username'] = $user;
}
if($err>0)
echo "invalid username or password";
else if($flag==1 && $type=="Guide")
echo "<script>location.href='guidehome.php'</script>";
else if($flag==1 && $type=="Researcher")
echo "<script>location.href='researcherhome.php'</script>";
else
echo"<FONT COLOR=WHITE>INVALID USERNAME OR PASSWORD</FONT>";
}
?>

Researcher_reg.php

UNIVERSITY INSTITUTE OF TECHNOLOGY, Kollam 2017


BIO SEQUENCE ANALYSER Page | 37

<html>
<head>
<script language="javascript" type="text/javascript">
function checkform()
{
var pwd=document.reg.pwd.value;
if (document.reg.name.value=="")
{
// something is wrong
alert('Please fill this area ');
document.reg.name.focus();
return false;
}else if (document.reg.mob.value=="")
{
// something is wrong
alert('please fill this area');
document.reg.mob.focus();
return false;
}
else if (document.reg.email.value=="")
{
// something is wrong
alert('please fill this area');
document.reg.email.focus();
return false;
}
else if (document.reg.Qualification.value=="")
{
// something is wrong
alert('please fill this area');
document.reg.Qualification.focus();
return false;

UNIVERSITY INSTITUTE OF TECHNOLOGY, Kollam 2017


BIO SEQUENCE ANALYSER Page | 38

}
else if (document.reg.Rarea.value=="")
{
// something is wrong
alert('please fill this area');
document.reg.Dsg.focus();
return false;
}
else if (document.reg.pwd.value=="")
{
// something is wrong
alert('please fill this area');
document.reg.pwd.focus();
return false;
}
else if (pwd.length<6)
{
// something is wrong
alert('Password must be atleast 6 characters');
document.reg.pwd.focus();
return false;
}
return true;
}
function alpha()
{
var letters = /^[A-Za-z ]+$/;
if(document.reg.name.value.match(letters))
{
return true;
}
else

UNIVERSITY INSTITUTE OF TECHNOLOGY, Kollam 2017


BIO SEQUENCE ANALYSER Page | 39

{
alert("Please check this field : Name");
document.reg.name.focus();
return false;
}
}
function num()
{
var num = /^[0-9]+$/;
if(document.reg.mob.value.match(num))
{
return true;
}
else
{
alert("Please check this field : Mobile No.");
document.reg.num.focus();
return false;
}
}
</script>
</head>
<body>
<div id=mnb><center>
<br><br><br>
<h2>Researcher Registration<hr></h2>
<form action="#" method=post name="reg" onSubmit="return checkform()" >
<div>
<center>
<pre>
<tr><td>Name : <input type=text name=name placeholder="First and Last name"
onblur="alpha()">

UNIVERSITY INSTITUTE OF TECHNOLOGY, Kollam 2017


BIO SEQUENCE ANALYSER Page | 40

<tr><td>Geneder : <input type="radio"name=gender value="male">


Male <input type="radio"name="gender" value="female"> Female<br>
<tr><td>DOB : <input type="date" name=dob> <br>
<tr><td>Mobile No. : <input type=text name=mob onblur="num()">
<tr><td>Location : <input type=text name=loc>
<tr><td>Email : <input type="email" name=email>
<tr><td>Qualification : <input type="text" name="Qualification">
<tr><td>Research Area : <input type="text" name="Rarea">
<tr><td>Password : <input type="password" name="pwd">
<tr><td><input type="Submit" name=submit ></form>
</pre>
</body>
</html>
<?php
if(isset($_POST["submit"]))
{
$name=$_POST['name'];
$gender=$_POST['gender'];
$dob=$_POST['dob'];
$mob=$_POST['mob'];
$Loc=$_POST['loc'];
$Email=$_POST['email'];
$Qu=$_POST['Qualification'];
$Res=$_POST['Rarea'];
$pass=$_POST['pwd'];
$conn=mysql_connect("localhost","root","");
mysql_select_db("techbio",$conn);
$sql="insert into researcher_reg(name,gen,DOB,Mob,location,email,qtn,Rarea)
values('$name','$gender','$dob','$mob','$Loc','$Email','$Qu','$Res')";
$s="insert into login values('$Email','$pass','Researcher','0')";
if(mysql_query($sql))
{

UNIVERSITY INSTITUTE OF TECHNOLOGY, Kollam 2017


BIO SEQUENCE ANALYSER Page | 41

mysql_query($s);
echo "<script>alert('Successfully Submitted')</script>";
echo "<script>location.href='home.html?msg=0'</script>";
}
else
{
echo "<script>alert('Please check the form')</script>";
}
}

Guide_Reg.php
<html>
<head>
<script language="javascript" type="text/javascript">
function checkform()
{
var pwd=document.reg.pwd.value;
if (document.reg.name.value=="")
{
// something is wrong
alert('Please fill this area ');
document.reg.name.focus();
return false;
}else if (document.reg.mob.value=="")
{
// something is wrong
alert('please fill this area');
document.reg.mob.focus();
return false;
}
else if (document.reg.email.value=="")
{

UNIVERSITY INSTITUTE OF TECHNOLOGY, Kollam 2017


BIO SEQUENCE ANALYSER Page | 42

// something is wrong
alert('please fill this area');
document.reg.email.focus();
return false;
}
else if (document.reg.Qualification.value=="")
{
// something is wrong
alert('please fill this area');
document.reg.Qualification.focus();
return false;
}
else if (document.reg.Rarea.value=="")
{
// something is wrong
alert('please fill this area');
document.reg.Dsg.focus();
return false;
}
else if (document.reg.pwd.value=="")
{
// something is wrong
alert('please fill this area');
document.reg.pwd.focus();
return false;
}
else if (pwd.length<6)
{
// something is wrong
alert('Password must be atleast 6 characters');
document.reg.pwd.focus();
return false;

UNIVERSITY INSTITUTE OF TECHNOLOGY, Kollam 2017


BIO SEQUENCE ANALYSER Page | 43

}
return true;
}
function alpha()
{
var letters = /^[A-Za-z ]+$/;
if(document.reg.name.value.match(letters))
{
return true;
}
else
{
alert("Please check this field : Name");
document.reg.name.focus();
return false;
}
}
function num()
{
var num = /^[0-9]+$/;
if(document.reg.mob.value.match(num))
{
return true;
}
else
{
alert("Please check this field : Mobile No.");
document.reg.num.focus();
return false;
}
}
</script>

UNIVERSITY INSTITUTE OF TECHNOLOGY, Kollam 2017


BIO SEQUENCE ANALYSER Page | 44

</head>
<body>
<center>
<br><br><br>
<h2>Guide Registration<hr></h2>
<form action="#" method=post name="reg" onSubmit="return checkform()" >
<div>
<center>
<pre>
<tr><td>Name : <input type="text" name=name onblur="alpha()">
<tr><td>Geneder : <input type="radio"name=gender value="male"> Male <input
type="radio"name="gender" value="female"> Female
<tr><td>DOB : <input type="date" name=dob>
<tr><td>Mobile No. : <input type=text name=mob onblur="num()">
<tr><td>Location : <input type=text name=loc>
<tr><td>Email : <input type="email" name=email >
<tr><td>Qualification : <input type="text" name="Qualification" >
<tr><td>Specialization : <input type="text" name="spl" >
<tr><td>Designation : <input type="text" name="Dsg" >
<tr><td>Password : <input type="password" name="pwd" >
<input type="Submit" name=submit ></form></div>
</pre>
</body>
</html>
<?php
if(isset($_POST["submit"]))
{
$name=$_POST['name'];
$gender=$_POST['gender'];
$dob=$_POST['dob'];
$mob=$_POST['mob'];
$Loc=$_POST['loc'];

UNIVERSITY INSTITUTE OF TECHNOLOGY, Kollam 2017


BIO SEQUENCE ANALYSER Page | 45

$Email=$_POST['email'];
$Qu=$_POST['Qualification'];
$spl=$_POST['spl'];
$des=$_POST['Dsg'];
$pass=$_POST['pwd'];
$conn=mysql_connect("localhost","root","");
mysql_select_db("techbio",$conn);
$sql="insert into guide_reg(name,gen,DOB,mob,location,email,qtn,spcl,dgnt)
values('$name','$gender','$dob','$mob','$Loc','$Email','$Qu','$spl','$des')";
$s="insert into login values('$Email','$pass','Guide','0')";
if(mysql_query($sql))
{
mysql_query($s);
echo "<script>alert('Successfully Submitted')</script>";
echo "<script>location.href='home.html?msg=0'</script>";
}
else
{
echo "<script>alert('Please check the form')</script>";
}
}

Researcherlist.php
<html>
<body>
<center>
<h3>Researchers</h3>
<hr>
</center>
<br><br><br>
<pre>
<table border=2 align=center>

UNIVERSITY INSTITUTE OF TECHNOLOGY, Kollam 2017


BIO SEQUENCE ANALYSER Page | 46

<tr><th>&nbsp&nbspResearcher
ID&nbsp&nbsp<th>&nbsp&nbsp&nbsp&nbsp&nbsp&nbspName&nbsp&nbsp&nbsp&nbsp
&nbsp&nbsp<th>&nbsp&nbsp&nbsp&nbsp&nbsp&nbsp&nbsp&nbsp&nbsp&nbsp&nbsp&
nbspEmail
ID&nbsp&nbsp&nbsp&nbsp&nbsp&nbsp&nbsp&nbsp&nbsp&nbsp&nbsp&nbsp<th>&nbs
p&nbsp&nbsp&nbsp&nbsp&nbsp&nbsp&nbspResearch
Area&nbsp&nbsp&nbsp&nbsp&nbsp&nbsp&nbsp&nbsp
<?php
$conn=mysql_connect("localhost","root","");
if (!$conn)
{
die('Could not connect: ' . mysql_error());
}
mysql_select_db("techbio",$conn);
$sql="select R_ID,name,email,Rarea from researcher_reg ";
$result = mysql_query($sql);
while($row = mysql_fetch_array($result))
{
$R_ID=$row['R_ID'];
$name=$row['name'];
$email=$row['email'];
$Rarea=$row['Rarea'];
echo"<tr align=center><td>$R_ID<td>$name<td>$email<td>$Rarea";
}
?>

UNIVERSITY INSTITUTE OF TECHNOLOGY, Kollam 2017


BIO SEQUENCE ANALYSER Page | 47

6. SCREEN SHOTS

Fig 1 Home Page

Fig 2 Researcher’s Home Page

UNIVERSITY INSTITUTE OF TECHNOLOGY, Kollam 2017


BIO SEQUENCE ANALYSER Page | 48

Fig 3 Research Guide Home page

Fig 4 Login Page

UNIVERSITY INSTITUTE OF TECHNOLOGY, Kollam 2017


BIO SEQUENCE ANALYSER Page | 49

Fig 5 Registration Home Page

Fig 6 Researcher Registration

UNIVERSITY INSTITUTE OF TECHNOLOGY, Kollam 2017


BIO SEQUENCE ANALYSER Page | 50

7. TESTING
7.1 UNIT TESTING
Unit testing is undertaken when a module has been coded and successfully reviewed.
Here we test each module separately in order to test a single module we need a complete
environment to provide all that is necessary for execution of the module. That is besides the
module under test, we will need the following in order to be able to test the module.

 The procedures belong to other modules that the module under test call.
 Non local data structures that the module accesses.
 A procedure to call the function of the module under test with appropriate parameters.

Black box testing


In black box testing a test cases are designed from an examination of the input or
output values only and no knowledge of design or code is required. The following are the two
main approaches to designing Black box test cases.

 Equivalence class partitioning.


 Boundary value analysis.

UNIVERSITY INSTITUTE OF TECHNOLOGY, Kollam 2017


BIO SEQUENCE ANALYSER Page | 51

7.2 INTEGRATION TESTING

The primary objective of integration testing is to test the module interfaces in order to
ensure that there are no errors in the parameter passing .when one module invokes another
module. During integration testing, different modules of a system are integrated in a planned
manner using an integration plan. Integration plan specifies the steps and the order in which
modules are combined to realize the full system. After each integration step, the partially
integrated system is tested.

7.3 SYSTEM TESTING


System tests are designed to validate a fully developed system to assure that it meets its
requirements. There are essentially three main kinds of system testing

1. Alpha testing.
Alpha testing refers to system testing carried out by the test team within the
developing organization

2. Beta testing
Beta testing is the system testing performed by a select group of friendly customers.

3. Acceptance testing
Acceptance testing is the system testing performed by the customer to determine
whether to accept or reject the delivery of the system.

UNIVERSITY INSTITUTE OF TECHNOLOGY, Kollam 2017


BIO SEQUENCE ANALYSER Page | 52

8. IMPLEMENTATION & MAINTENANCE


8.1 IMPLEMENTATION PLAN
Implementation is the stage of the project when the theoretical design is turned into a
working system. If the implementation stages is not carefully planned and controlled it can
cause problem. Thus it can be considered to be the most crucial stage in achieving a
successful new system and give confidence to the users that the new system will work and
effective. The implementation stage is a system in its own right. It involves careful planning,
investigation of the current system and its constraints in implementation, design of methods
to achieve the changeover procedures, training of staffs in the changeover methods.
The more complex system is being implemented the more involved will be the system
analysis and design effort required for implementation. Implementation is concerned with
those tasks leading immediately to a fully operational task. It involves programmers, users
and operations management but its planning and timing is a prime function of system
analysis. It includes the final testing of the complete system to user satisfaction, and
supervision of the initial operation of the new system.
Implementation is the process of converting a new or revised system into operation. It
is the key stage in achieving a successful new system because, usually it reveals a lot of up
heal the use department. It must before be carefully planned and controlled. Apart from
planning the two major tasks of preparing for implementation are education and training of
users and testing of the system. Education of users should really takes place much earlier in
the project that is, when they are involved in the investigation and design work. Training has
to be given to the staff regarding the new system. Once staff has been trained, the system can
be tested.
Implementation is the stage of the project where the theoretical design is turned into
working system or it is the key stage in achieving a successful new system, because usually it
involves a lot of up heal in the user department. Therefore it must be carefully planned and
controlled. It can also be considered to be the most crucial stage in achieving a successful
new system and in giving he user confidence that the new system will work and be effected.
Implementation is the final important phase. It is the phase where theoretical design is
turned into working system, which works for the user in the most effective manner. It
involves careful planning, Investigation of the present system and constraints involved, user
training, system testing and successful running of developed proposed system. The
implementation process begins with preparing a plan for the implementation of the system.
According to this plan the activities can be carried out, discussions made regarding the
equipment, resources and additional equipment has to be acquired to their needs. The testing
phase involves the testing of a system using various kinds of data. This method also uses the
greatest security since the old system can take over if the errors are found or inability to
handle certain type transaction while using the new system.
The definition of software maintenance can be given by describing four activities that
are undertaken after the program is released for use. The first maintenance activity occurs
since it is unreasonable to assume that software testing will uncover all errors in a large

UNIVERSITY INSTITUTE OF TECHNOLOGY, Kollam 2017


BIO SEQUENCE ANALYSER Page | 53

software system. The process of including diagnosis and correction of one or more errors is
called corrective maintenance.
The second activities that contribute to the definition of maintenance occur since rapid
change is encountered in very aspects of computing. Therefore adaptive maintenance
modifies software to properly interface with a changing environment. The third activity
involves recommendations for new capabilities; modifications to the existing function and
general enhancement when the software is used. To satisfy request perspective maintenance
is performed.

UNIVERSITY INSTITUTE OF TECHNOLOGY, Kollam 2017


BIO SEQUENCE ANALYSER Page | 54

9. FURTHER ENHANCEMENT
In this section, we present an enhanced system of our system. Enhancing means
adding, modifying or developing the code to support the changes in the specification. It is the
process of adding new capabilities such as reports, new interfaces with other systems and
new features such as better screen or report layout. The proposed system is developed and
tested with some amount of sample data which satisfy all the requirements. It has high degree
of accuracy, user friendliness and efficiency. The system is flexible and changes can be made
without much difficulty. Further enhancement and extensions can be made in the system to
make overall work easier. Concerning with this software there are many further enhancement
as the technology develops.

UNIVERSITY INSTITUTE OF TECHNOLOGY, Kollam 2017


BIO SEQUENCE ANALYSER Page | 55

APPENDIX I
MINUTES OF MEETING

MEETING 1

Date : 06-Jan-2017

Time : 11.00 am

Location : Library, UIT

Present

Name

Abhijith R. B

Afsal Rahim

Staff : Mr. Godwin Sylvester S.B

Discussions & Decisions

Project title discussion

We discussed about an apt name for our project. Last we concluded to select the name "Bio
Sequence Analyser".

About front-end and back-end platform

We selected our front-end as PHP and SQL as back-end.

Schedule next meeting

The team meeting will be on 09-Jan-2017

UNIVERSITY INSTITUTE OF TECHNOLOGY, Kollam 2017


BIO SEQUENCE ANALYSER Page | 56

MEETING 2

Date : 10-Jan-2017

Time : 1.20 pm

Location : Library, UIT

Present

Name

Abhijith R. B

Afsal Rahim

Staff : Mr. Godwin Sylvester S.B

Discussions & Decisions

Requirement needed for the system

We decide that the system must require minimum 128 MB RAM and 40 GB hard disk
capacity.

Schedule next meeting

The team meeting will be on 13-Jan-2017

MEETING 3

Date : 06-Feb-2017

Time : 10.00 am

Location : Library, UIT

Present

Name

Abhijith R. B

Afsal Rahim

Staff : Mr. Godwin Sylvester S.B

UNIVERSITY INSTITUTE OF TECHNOLOGY, Kollam 2017


BIO SEQUENCE ANALYSER Page | 57

Discussions & Decisions

Design for the system

We choose a standard design for our Project

Schedule next meeting

The team meeting will be on 12-Feb-2017

MEETING 4

Date : 08-March-2017

Time : 2.00 pm

Location : Library, UIT

Present

Name

Abhijith R. B

Afsal Rahim

Staff : Mr. Godwin Sylvester S.B

Discussions & Decisions

Validation of the forms in our project.

Validated various forms associated to our project and debug the errors.

Schedule next meeting

The team meeting will be on 14-Feb-2017

UNIVERSITY INSTITUTE OF TECHNOLOGY, Kollam 2017


BIO SEQUENCE ANALYSER Page | 58

APPENDIX II

GANTT CHART

UNIVERSITY INSTITUTE OF TECHNOLOGY, Kollam 2017


BIO SEQUENCE ANALYSER Page | 59

BIBLIOGRAPHY
Book Reference
1. Rajib Mall, Fundamentals of Software Engineering, Eastern Economy Edition, Third
Edition, Year 2009.

2. Roger S Pressman, Software Engineering , TataMcgrawHill, Fifth Edition, Year


2004.

3. Jiawei Han & Micheline Kamber, Data Mining Concepts And Techniques, Second
Edition

4. V. Rajaraman, Analysis and Design of Information Systems, Eastern Economy


Edition, Third Edition, Year 2011.

5. Margaret H Dunham, Data Mining: Introductory and Advanced Topics, Pearson


Education, First Edition, Year 2008

Web Reference
1. www.w3schools.com/php
2. www. php.net
3. www.biophp.org
4. www.bioinformatics.org
5. www.rcsb.org

UNIVERSITY INSTITUTE OF TECHNOLOGY, Kollam 2017

You might also like