About Bioinformatics Courses under DOEACC

The course in Bioinformatics (BI) is being introduced at various levels for the benefit of students aspiring
to become Bioinformatics Professionals. The Society has formulated the Scheme with the active
involvement of leading experts from reputed Institutions/organisations. Following levels of courses are
available under the Scheme:

Bioinformatics “O” level (BI-O) Assistant Programmers, Technical Assistants, Information Assistants

Bioinformatics “A” level (BI-A) Programmers, Training Faculty

Bioinformatics “B” level (BI-B) Senior Programmers, Systems Analysts, Scientists, Research
Associates

Bioinformatics “C” level (BI-C) Research Scientist, Strategy Manager, Database Architect,
Consultant, Design specialist.

Bioinformatics “O” level (BI-O) Syllabus:

Module Category Subject

BI-M1-R0 Core Foundation Course in Modern Biology
BI-M2-R0 Core Basic Bioinformatics
BI-M3-R0 Core IT Tools and Application
BI-M4-R0 Elective One to be chosen out of the following:
BI-M4.1-R0 Elective 1 Programming and Problem solving
through C
BI-M4.2-R0 Elective 2 Programming through Visual Basic

PR-1 Practical I on Basic Bioinformatics

BI-PJ Project on Bioinformatics

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Bioinformatics “A” level (BI-A) Syllabus:

Semester-I

Module Category Subject

BI-A1-R0 Core Foundation Course in Modern Biology
BI-A2-R0 Core Basic Bioinformatics
BI-A3-R0 Core IT Tools and Application
BI-A4-R0 Core Programming and Problem solving
through C
BI-A5-R0 Core Basic Mathematics, Probability and
Statistics

Semester-II

Module Category Subject

BI-A6-R0 Core Introduction to Database and Web enabling technologies
BI-A7-R0 Core PERL/PYTHON Programming and applications to Bioinformatics
BI-A8-R0 Core Introduction to Object Oriented programming through JAVA
BI-A9-R0 Core Elements of protein Sequence, Structure and modelling
BI-A10-R0 Core Basics of Genomics and Proteomics

PR-1 Practical I (common to O-Level Basic Bioinformatics )

PR-2 Practical II on PERL(BI-A7-R0) and Java(BI-A8-R0)

BI-PJ Project (On Bioinformatics)

Exemptions: Students who have qualified BI-O-R0 would get exemption in the following subjects:-

BI-A1-R0
BI-A2-R0
BI-A3-R0
BI-A4-R0, If the candidate has qualified equivalent paper at BI-O level
(Programming and Problem solving through C)

PR-1

2
Bioinformatics “B” level (BI-B) Syllabus:

COURSE STRUCTURE OF THE “B LEVEL (BIOINFORMATICS)”

S. No. Paper Code Title

Semester I
1. B1.1 IT Tools and Application
2. B1.2 Basic Mathematics, Probability and Statistics
3. B1.3 Programming and Problem solving through C
4. B1.4 Basic Bioinformatics
5. B1.5 Foundation Course in Modern Biology

Semester II
6. B2.1 Introduction to Database and Web enabling technologies
7. B2.2 PERL/PYTHON Programming and applications to Bioinformatics
8. B2.3 Introduction to Object Oriented programming through JAVA
9. B2.4 Elements of protein Sequence, Structure and modelling
10. B2.5 Basics of Genomics and Proteomics

Semester III
11. B3.1 Computer Organization and Distributed computing
12. B3.2 Probability and Information theory
13. B3.3 Computational methods in Biomolecular sequence analysis
14. B3.4 Discrete Mathematics

Semester IV
15. B4.1 Statistical methods in Bioinformatics
16. B4.2 Biomoleculer Structure and Dynamics
17. B4.3 Data Structure and Algorithms
18. B4.4 Computational Genomics

Semester V
19. B5.1 Optimisation, Machine Learning and Computational Intelligence
20. B5.2 Object Technology for Bioinformatics
21. B5.3 Computational Proteomics and Gene Expression studies

Optional Course
22. B5.4.1 Computer aided Molecular Modeling and Drug Discovery
(OR)
B5.4.2 Chemoinformatics

Semester VI Project

Note: Theory = 60 hours and Practical = 60 hours

Practicals:

Each course module has a practical component and the same will be carried out with software
recommended by DOEACC from time to time.

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SEMESTER – I

4
 BI-M3/A3/B1.1-R0: IT TOOLS AND APPLICATIONS

Objective of the Course

This course has been designed to provide an introduction to Information Technology and IT Tools. The
student will become IT literate, and will understand the basic IT terminology. The students will be able to
understand the role of Information Technology and more specifically computers, communication
technology and software in the present social and economic scenario.

The course has focus on the following:

♦ Overview of the Information Technolgy

♦ Computer Organization
♦ Computer Operating System and Software
♦ MS Windows, LINUX, Word Processing and Spreadsheet tools
♦ Multimedia and Presentation Packages

Outline of Course

Minimum No. of
S. No. Topic
Hours
1. Computer Appreciation 04
2. Computer Organization 13
3. Operating System 13
4. Word Processing 10
5. Spreadsheet Package 10
6. Presentation Package 06
7. Information Technology and Society 04
Lectures = 60
Practical / Tutorials = 60
Total = 120

Detailed Syllabus

1. Computer Appreciation 4 Hrs.

Characteristics of Computers, Input, Output, Storage units, CPU, Computer System, Binary
Number System Binary to Decimal Conversion, Decimal to Binary Conversion, Binary Coded
Decimal (BCD) Code, ASCII Code

2. Computer Organisation 13 Hrs.

2.1 Central Processing Unit 1 Hr.

Control Unit, Arithmetic Unit, Instruction Set, Register, Processor Speed

2.2 Memory 3 Hrs.

Main Memory: Storage Evaluation Criteria, Memory Organization, capacity, RAM, Read
Only Memories. Secondary Storage Devices: Magnetic Disks, Floppy and Hard Disks,
Optical Disks CD-ROM, Mass Storage Devices.

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 2.3 Input Devices 2 Hrs.

Keyboard, Mouse, trackball, joystick, Scanner, OMR, Bar-code reader, MICR Digitizer,
Card Reader, Voice Recognition, web cam, video cameras.

2.4 Output Devices 2 Hrs.

Monitors, Printers – Dot matrix, inkjet, laser, plotters, Computer output Micro-Film (COM),
Multimedia Projector, speech synthesizer, dumb, smart and intelligent terminal.

2.5 Multimedia: 2 Hrs.

What is Multimedia, Text, Graphics, Animation, Audio, images, Video, Multimedia

Application in Education, Entertainment, Marketing.

2.6 Computer Software 3 Hrs.

Relationship between Hardware and Software ; system software, application software,

compiler, names of some high level languages, free domain software.

3. Operating Systems 13 Hrs.

Disk Operating System

Simple DOS Commands, Simple File Operations, Directory related Commands

Microsoft Windows

An overview of different versions of Windows, Basic Windows elements, Files

management through Windows.

Using essential accessories: Systems tools – Disk cleanup, Disk defragmenter,

Entertainment, Games, Calculator, Imaging – Fax, Notepad, Paint, WordPad.

Linux

An overview of Linux , Basic Linux elements: System Features, Software Features. File
Structure,
File handling in Linux, Installation of Linux: H/W, S/W requirements, Preliminary steps
before installation, specifics on Hard drive repartitioning and booting a Linux System.

4. Word Processing 10 Hrs.

Word Processing concepts: Saving, Closing, Opening an existing document, Selecting text,
Editing text, Finding and replacing text, printing documents, Creating and Printing Merged
documents, Character and Paragraph Formatting, Page Design and Layout.

Editing and Proofing Tools: Checking and correcting spellings. Handling Graphics. Creating
Tables and Charts. Document Templates and Wizards*.

5. Spreadsheet Package 10 Hrs.

Spreadsheet Concepts. Creating, Saving and Editing a workbook, Inserting, Deleting work
Sheets, entering data in a cell/formula. Copying and Moving data from selected cells, Handling

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 operators, in Formulae, Functions: Mathematical. Logical, Statistical, Text, Financial, Data ad
Time Functions, Using Function wizard.

Formatting a Worksheet : Formatting Cells -- Changing data alignment, Changing date,

number, character, or currency format, changing font, adding borders and colors, printing
worksheets, Charts and Graphs – Creating, Previewing, Modifying Charts.

Integrating word processor, spread sheets, web pages*.

6. Presentation Package 6 Hrs.

Creating, Opening and Saving Presentations, Creating the Look of Your Presentation, Working in
Different Views, Working with Slides, Adding and Formatting Text, Formatting Paragraphs,
Checking Spelling and Correcting Typing Mistakes, Making Notes Pages and Handouts, Drawing
and Working with Objects, Adding Clip Art and Other Pictures, Designing Slide Shows, Running
and Controlling a Slide Show, Printing Presentations*.

7. Information Technology and Society 4 Hrs.

Application of Information Technology in Railways, Airlines, Banking, Insurance, Inventory

Control, Financial Systems, Hotel Management, Education, Video Games, Telephone exchanges,
Mobile Phones, Information Kiosks, Special effects in Movies.

* Note: The underlying concepts may be illustrated using MS Office Package.

RECOMMENDED BOOKS

MAIN READING

1. P. K. Sinha and P. Sinha (2002), “Foundations of Computing”, First Edition, BPB Publication.

2. S. Sagman, “Microsoft Office 2000 for Windows”, Second Indian Print, 2000, Pearson
Education.

SUPPLEMENTARY READING

1. Turban, Mclean and Wetherbe, “Information Technology and Management”, Second Edition,
2001, John Wiley & Sons.

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 BI-A5/B1.2-R0: BASIC MATHEMATICS, PROBABILITY AND STATISTICS

Objective of the Course

Mathematical and statistical frameworks are being increasingly employed to understand and investigate
biological processes. These frameworks helps in analyzing vast amount of datasets generated from
genome and related projects. It is thus essential to introduce basic concepts of mathematics, probability
and statistics early within the Bioinformatics curriculum. This course will enable students to understand
and appreciate computational problems in proper perspective. In addition, this course will provide a
foundation for pursuing higher level courses in Computational Biology.

Outlines of Course

S. No. Topics Minimum No. of hours

1. Real Numbers 2
2. Set, Relation and Function 3
3. Limits 4
4. Binomial Theorem 2
5. Calculus 12
6. Matrices and Vectors 5
7. Complex Numbers 2
8. Elementary Statistics 6
9. Regression and Correlation 4
10. Probability 8
11. Random Variables and Probability Distribution 12

Lectures = 60
Practicals/ Tutorials = 60
Total = 120

Detailed Syllabus

1. Real Numbers 2 Hours

Different kinds of number Integer, Rational and Irrational

Surds and their properties, Fractional indices

2. Set, Relation and Function 3 Hours

Set, Product sets

Relations
Functions (Polynomials, Trigonometric, Exponential)
Graphical Representation of Functions

3. Limits 4 Hours

Sequences
Limits of sequences
Series
Limits of functions

8
4. Binomial Theorem 2 Hours
n
Expanding (x+y)
Binomoal Coffiecients, Binomial Theorem

5. Calculus 12 Hours

a) Differentiation ….5 Hours

Calculating gradients of chords
First order and higher derivatives
Applications : Increasing and Decreasing
Functions, Maximum and Minimum points
Derivatives as rates of change

b) Integration ….5 Hours

Finding a function from its derivative
Definite integral
Calculating Areas, Volumes

c) Differential Equations ….2 Hours

Forming differential equations
First order differential equation, growth equation
Applications

6. Matrices and Vectors 5 hours

Matrix algebra, Determinants

Applications
Vector in space
Applications

7. Complex Numbers 2 hours

Extending the number system

Operations with complex numbers

8. Elementary Statistics 6 hours

a) Representation of data :
Discrete Data, Continuous data
Histogram, Polygons, Frequency Curves
b) The Mean,
Variability of data –
The standard deviation
c) Median, quantiles, percentile
d) Skewness
e) Box and Whisker diagrams (box plots)

9. Regression and Correlation 4 hours

Scatter diagrams
Regression function
Linear correlation and regression lines
Product moment correlation coefficient

9
10. Probability 8 hours

Experimental probability ….. 2 hours

Probability when outcomes are equally likely
Subjective probabilities
Probabilities law ….. 4 hours
Probability rules for combined events
Conditional probability and independent events
Probability trees ….. 2 hours
Bayes’ theorem

11. Random Variables and Distributions 12 hours

a) Discrete and Continuous Random Variables ….. 5 hours
Cumulative distribution function
Probability mass function and Probability Density function
Expectation of random variables – Experimental
Approach and theoretical approach
Expectation of X and variance of X
Expectation of function E[g(X)]

b) Bernoulli Distribution 3 hours

Binomial Distribution
Poisson Distribution

c) Uniform Distribution 4 hours

Normal Distribution
Normal approximation to Binomial
Distribution
Central limit theorem

RECOMMENDED BOOKS

MAIN READING

1. H. Nell and D. Quadling, ‘Pure Mathematics (Advanced Level Mathematics)’. Vol. 1,2,3,
Cambridge University Press 2002.
rd
2. Edward Batschelet. ‘Introduction to Mathematics for Life Scientists’, 3 Edition, Springer – Verlag,
1992
th
3. J. Crawshaw and J. Chambers’, ‘Advanced level Statistics’, 4 Edition, Nelson Thornes, 2002

SUPPLEMENTARY READING

1. Sheldon Ross, ‘A first Course in Probability’, Sixth Edition, Pearson Education Asia, 2002

2. S. Dobbs and J. Millser, ‘Statistics (Advanced Level mathematics);, Cambridge University Press
2002

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 BI-M4.1/A4/B1.3-R0: PROGRAMMING AND PROBLEM SOLVING THROUGH ‘C’ LANGUAGE

Objective of the Course

The objectives of this course are to make the student understand programming language, programming,
concepts of Loops, reading a set of Data, stepwise refinement, Functions, Control structure, Arrays. After
completion of this course the student is expected to analyse the real life problem and write a program in
‘C’ language to solve the problem. The main emphasis of the course will be on problem solving aspect,
i.e. developing proper algorithms.

♦ After completion of the course the student will be able to

♦ develop efficient algorithms for solving a problem
♦ Use the various constructs of a programming language viz. conditional, iteration and recursion.
♦ Implement the algorithms in ‘C’ language
♦ Use simple data structures like arrays, stacks and linked list in solving problems
♦ Handling File in ‘C’.

Outline of Course

Minimum No. of
S.No. Topic
Hours
1. Introduction to Programming 04
2. Algorithms for Problem solving 12
3. Introduction to ‘C’ language 04
4. Conditionals and loops 08
5. Arrays 06
6. Functions 06
7. Structures and Unions 06
8. Pointers 06
9. Self Referential Structures and Linked Lists 04
10. File Processing 04
Lectures = 60
Practicals/ Tutorials = 60
Total = 120

Detailed Syllabus

1. Introduction to Programming 4 hours

The Basic Model of Computation, Algorithms, Flow-Charts, Programming Languages,

Compilation, Linking and Loading, Testing and Debugging, Documentation

2. Algorithms for Problem Solving 12 hours

Exchanging values of two variables, summation of a set of numbers, Decimal Base to Binary
Base conversion, Reversing digits of an Integer, GCD (Greatest Common Division) of two
numbers, Test whether a number is prime, Organise numbers in ascending order, Find square
root of a number, factorial computation, Fibonacci sequence, Evaluate ‘sin x’ as sum of a series,
Reverse order or elements of an array, find Largest number in an array, Print elements of upper
triangular matrix, multiplication of two matrices, Evaluate a Polynomial.

11
3. Introduction to ‘C’ language 4 hours

3.1 Character set, Variable and Identifiers, Built-in-Data Types, Variable Definition
3.2 Arithmetic operators and Expressions, Constants and Literals
3.3 Simple assignment statement, Basic input/output statement
3.4 Simple ‘C’ programs

4. Conditional Statements and Loops 8 hours

4.1 Decision making within a program

4.2 Conditions, Relational Operators, Logical Connectives
4.3 if statement, if-else statement
4.4 Loops: while loop, do while, for loop, nested loops, infinite loops, switch statement,
structured programming

5. Arrays 6 hours

One dimensional arrays: Array manipulation; Searching, Insertion, Deletion of an element from an
array; Finding the largest /smallest element in an array; Two dimensional arrays, Addition/
Multiplication of two matrices, Transpose of a square matrix; Null terminated strings as array of
characters, Representation sparse matrices

6. Functions 6 hours

Top down approach of problem solving, Modular programming and functions, Standard Library of
C functions, Prototype of a function: Formal parameter list, Return Type, Function call, Block
structure, Passing arguments to a function: call by reference, call by value, Recursive Functions,
arrays as function arguments

7. Structures and Unions 6 hours

Structure variables, initialization, structure assignment, nested structure, structures and functions,
structures and arrays: arrays of structures, structures containing arrays, unions

8. Pointers 6 hours

Address operators, pointer type declaration, pointer assignment, pointer initialization, pointer
arithmetic, functions and pointers, Arrays and Pointers, pointer arrays

9. Self Referential Structures and Linked Lists 4 hours

Creation of a singly connected linked list, traversing a link list, Insertion into a linked list, Deletion
from a linked list

10. File Processing 4 hours

Concepts of Files, File opening in various modes and closing of a file, Reading from a file, Writing
onto a file

12
RECOMMENDED BOOKS

MAIN READING

1. Byron Gottfried, “Programming with C” Second Edition, Tata McGrawhill, 2000

2. R. G. Dromey, “How to solve it by Computer”, Seventh Edition, 2001, Prentice Hall of India

SUPPLEMENTARY READING

1. E. Balaguruswami, “Programming with ANSI-C”, First Edition, 1996, Tata McGrawhill

2. A. Kamthane, “Programming with ANSI & Turbo C”, First Edition, 2001, Pearson Education

3. Venugopal and Prasad, “Programming with ‘C’”, First Edition, 1997, Tata McGrawhill

4. B. W. Kernighan & D. M. Ritchie, “The C Programming Language”, Second Edition 2001, Prentice
Hall of India

BI-M2/A2/B1.4-R0: BASIC BIOINFORMATICS

Objective of the Course

On completion of this course, students will have basic knowledge of sources of sequences and protein
structure data, an understanding of the relevance and importance of this data, and some exposure to
basic algorithms used for processing this data.

Outline of Course

S. No. Topic Minimum No. of

Hours
1 Introduction to Genes and Proteins 10
2 Introduction to Internet Use and Search Engines 5
3 Genomic Sequence Information Sources 10
4 Protein Structure Information Sources 10
5 Introduction to Data Generating Methods 5
6 Sequence and Phylogeny Analysis 20
Lecture = 60
Practicals/Tutorials = 60
Total = 120

Detailed Syllabus

1. Introduction to Genes and Proteins 10 hours

Genome Sequences
ORFs, Genes, Introns, Exons, Splice Variants
DNA/RNA Secondary Structure Triplet Coding
Protein Sequences
Protein Structure: Secondary, Tertiary, Quaternary

13
 The notion of Homology

2. Introduction to Internet Use and Search Engines 5 hours

WWW, HTML, URLs

Browsers: Netscape / Opera / Explorer
Search Engines Google, PUBMED

3. Sequence Information Sources 10 hours

EMBL
GENBANK
Entrez
Unigene
Understanding the structure of each source and using it on the web

4. Protein Information Sources 10 hours

PDB
SwissProt
TrEMBL
Understanding the structure of each source and using it on the web

5. Introduction to Data Generating Techniques 5 hours

Restriction Enzymes, Gel Electrophoresis, Chromatograms
Blots, PCR, Microarrays, Mass Spectrometry
What data each generates, and what bioinformatic problems they pose.

6. Sequence and Phylogeny Analysis 20 hours

Detecting Open Reading Frames ….2 hours
Outline of Sequence Assembly ….3 hours
Mutation Matrices ….2 hours
Pairwise Alignments ….2 hours
Introduction to BLAST, using it on the web, interpreting results ….4 hours
Multiple Sequence Alignment ….3 hours
Phylogenetic Analysis ….4 hours

RECOMMENDED BOOKS

MAIN READING

Theory

1. D. Baxevanis and F. Oulette, (2002) “Bioinformatics : A practical guide to the analysis of genes
and proteins”, Wiley Indian Edition

2. Cynthia Gibas and Per Jambeck (2001), “Developing Bioinformatics Computer Skills”. O’Reilly
press, Shorff Publishers and Distributors Pvt. Ltd., Mumbai.

3. Bryan Bergeron MD (2003), “Bioinformatics Computing”. Prentice Hall India (Economy Edition)

4. Stuart Brown (2000) “Bioinformatics – A biologists guide to Biocomputing and Internet”. Eaton
Publishing

14
Practical

1. Jean-Michel Claverie and Cedric Notredame (2003) Bioinformatics – A Beginners Guide. Wiley –
Dreamtech India Pvt. Ltd.

SUPPLEMENTARY READING

Theory

1. T. K. Attwood & D. J. Parry-Smith (2001), “Introduction to Bioinformatics”, Pearson Education Ltd,

Low Price Edition.

2. Bioinformatics: Sequence and Genome Analysis. D. W. Mount (2001) Cold Spring Harbor
Laboratory Press.

3. Arthur M. Lesk (2002) “Introduction to Bioinformatis” Oxford University Press

BI-M1/A1/B1.5-R0: FOUNDATION COURSE IN MODERN BIOLOGY

Objective of the course

The objective of this foundation course is to familiarize students to basic terminology and concepts in the
subject. Unifying concepts and theories pointed out and stressed wherever applicable.

After completion of this course students should be able to

• Understand the underlying basic concepts in biology

• Be familiar with basic terminology
• Relate to the functioning of cellular machinery
• Appreciate the role of heredity and evolution in our ecology

Outline of Course

S. No. Topic Minimum No. of

Hours
1 General Biology 6
2 Basics of Cell Biology 8
3 Introductory Life Science – Botany and Zoology 6
4 Introduction to Human Biology 8
5 General Microbiology 6
6 Basics of Genetics and Evolution 10
7 Basic Molecular Biology I – Nucleic acids (DNA and RNA) 10
8 Basic Molecular Biology II – Proteins 6
Lecture = 60
Practicals/Tutorials = 60
Total = 120

15
 Detailed Syllabus

1. General Biology 6 hours

The nature of life, definition of life, characteristics of life, differences between animals and plants,
principal divisions in biology, importance of biology

2. Basics of Cell Biology 8 hours

Definition of Cell – fundamental cell types, difference between prokaryotic and eukaryotic cell
types, cell structure, cell wall, plasma membrane, different organelles and their function. Cell
division stages, chromosome structure, human chromosomes, sex chromosome.

3. Introductory Life Science -- Botany and Zoology 6 hours

What is a tissue, classification of tissue, meristematic tissue, intercellular space.

Reproduction and development of seed and non-seed plants, levels of organization, form
and function of systems, and a survey of major taxa.

4. Introduction to Human Biology 8 hours

Types of tissue in human : connective tissue, supporting tissues fluid tissue, muscular tissue,
nerve tissue, secretory tissue.
Human respiration : respiratory organs, mechanism of breathing in man, composition of different
respiratory gases, compartment of lung, gas exchange in lungs, transport of gases during
respiration, diseases of respiratory system. Human nutrition: Salivary glands, function of saliva,
swallowing process, digestion in stomach, secretory cells of stomach, digestion in small intestine,
pancreas, liver, bile, role of bile in fat digestion.

Human circulation : heart, blood flow control, diseases of heart and circulatory system. Human
excretion: Function of kidney, large intestine, summary of excretory substances, diseases related
to excretory system. Movement and locomotion: Organs responsible for movement, joints, bones
and muscles involved in walking, different sequences during locomotion.

Reproduction: Formation of sperm and ova, fertilization, Hormones: Regulation of hormone

secretion

5. General Microbiology 6 hours

Microbes in Our Lives: Definition of microorganisms, role in ecological balance, microorganisms

living in humans and animals, their role, microorganisms used to produce food and chemicals,
disease causing microorganisms.

A Brief History of Microbiology: Robert Hookes observation in 1665, Antoni van

Leeuwwenhoek sees microorganisms using a simple microscope (1673), Rudolf Virchow
introduced the concept of biogenesis: (1858). Pasteur’s discoveries (1861). Alexander Fleming’s
Penicillin discovery (1928). Penicillin has been used clinically an as antibiotic since the 1940s.

Fermentation and Pasteurization, Vaccination, Recombinant DNA Technology

Naming and Classifying of Microorganism

In a nomenclature system designed by Carolus Linnaeus (1735), each living organism is

assigned two names, The two names consist of a genus and a specific epithet, both of which are
underlined or italicized. All organisms are classified into Eubacteria, Archaea and Eucarya.
Eucarya includes Protista, Fungi, Plantae and Animalia.

16
 The diversity of Microorganisms

Bacteria, Fungi, Protozoa, Algae, Viruses, Multicelluer Animal Parasites

6. Basics of Genetics and Evolution 10 hours

Mendel’s work and experiments, gene bearer of heredity character, chemical basis of heredity.

Stages of evolution, origin of life, evidences of evolution from plant and animal kingdom. Genome
sequencing techniques.

7. Basic Molecular Biology I – Nucleic Acids (DNA and RNA) 10 hours

Chemical structure, hybridization, double helical structures, replication, concepts of gene and
genetic code, transcription and translation, mutations and its implications, Polymerase Chain
Reaction.

8. Basic molecular Biology II – Proteins 6 hours

Amino acid structure, chemical nature of residues, polymeric chain and folding, concepts of pH,
pKa, buffer, aqueous medium.

RECOMMENDED BOOKS

MAIN READING

1. Biological Science, Third Edition, N. P. O Green, G. W. Stout, D. J. Taylor, Editor, R. Soper,

Cambridge Low priced Edition
rd
2. Molecular Biology of the Cell, 3 Edition, Bruce Alberts et al., Garland Publishing, New York.
th
3. Lehninger Principles of Biochemistry, 4 Edition, David Nelson and Michael M Cox, Freeman
Publishers, 2004

SUPPLEMENTARY READING

1. DNA Structure and Function, R. R. Sinden, Academic Press, San Diego (1994)

2. Genes VIII Benjamin Lewin, Oxford University Press

17
SEMESTER – II

18
 BI-A6/B2.1-R0: INTRODUCTION DATABASE AND WEB ENABLING TECHNOLOGIES

Objective of the course

On completion of this course students will have adequate knowledge of different data models, basic
principles of data base management and basic web enabling technologies. Students will learn how to
design a database system, various normalization techniques and some useful query language. Students
will be able to develop web based applications to retrieve information from data bases. They should also
be able to design their own web sites, install web server, and do the relevant administrative tasks.

Outline of Course

S. No. Topic Minimum No. of

Hours
1 Introduction to databases 5
2 Entities Relationship model 4
3 Relational Algebra and Calculus 7
4 Issues in designing relational databases 6
5 Query language and query optimization 10
6 Database system architecture 4
7 Introduction to ASN.1 and NCBI data model 4
8 Basics of Internet and WWW 3
9 Web server 6
10 HTML 8
11 Introduction to XML and its difference with HTML 3
Lectures = 60
Practicals/Tutorials = 60
Total = 120

Detailed Syllabus

1. Introduction to Databases 5 hours

Why Database systems, Data abstraction and data models, Instances and schemas, Database
Administrator,
Data Definition and manipulation languages, brief introduction to network and hierarchical
models.

2. Entitles Relationship model 4 hours

Entity and entity sets, relationships and relationship sets,, E-R diagram, reducing E-R diagrams to
Tables and trees.

3. Relational Algebra and Calculus 7 hours

Relational algebraic operations such as select, project, union, set difference, Cartesian product,,
intersections, natural join, division, generalized projection, outer join etc., tuple relational calculus,
domain relational calculus.

4. Issues in designing relational databases 6 hours

Pitfalls in relational database design, decomposition, importance of normalization, functional

dependencies, Boyce-Code Normal form, third normal form and fourth normal form.

19
5. Query language and query optimization 10 hours
Domain types in SQL, Schema definition in SQL, Types of SQL commands, SQL operators,
tables, views, indexes, aggregate functions, insert, delete and update operations, join, union,
intersection, minus etc. in SQL, queries, sub-queries, equivalence of queries.

6. Database system architecture 4 hours

Introduction to centralized system, client server system, parallel system and distributed system.

7. Introduction to ASN.1 and NCBI data model 4 hours

Why specialized data model is required for biological sequences, different data types supported
by ASN.1and how they are used for storage of different types of information reading of NCBI data
using freely available NCBI toolbox.

8. Basics of Internet and WWW 3 hours

Introduction to Internet, TCP/IP, WWW, FTP, registration with ISP, Internet connection wizard,
URL http.

9. Web server 6 hours

Role of Web Server, a brief introduction to Apache, Introduction to PSW, capabilities of PSW,
installation of PSW, role of CGI program, configuring PSW for Perl / CGI, configuring system Data
Source name (DSN), publishing dynamic applications, creating web pages from information
contained in a data base, creation of internet database connection file, simple CGI programming
using Perl for simple form processing, use of ODBC drivers to connect a database – role of
internet database connector (.idc)files and HTML (.htx)files.

10. HTML 8 hours

Introduction, common tags, creation of hyperlink, incorporation of images, Tables, Frames,
formatting text with font.

Dynamic HTML, cascading style sheets, creation of background images, HTML object model,
dynamic positioning, direct animation path control.

11. Introduction to XML and its differences with HTML 3 hours

RECOMMENDED BOOKS

MAIN READING

1. H. M. Dietel, P. J. Dietel and T. R. Nieto, Internet and World Wide Web – how to program, Pearson
Education India
2. A. Silberschatz, H. F. Korth and S. Sudarshan, Database System Concepts, McGraw Hill
International
3. Zoe’Lacroix and critchlow. Bioinformatics : Managing scientific data. Morgan Kaufmann Publishers
2004.

SUPPLEMENTARY READINGS

1. A. Leon and M. Leon: Database Management Systems, Leon Vicas

2. C. J. Date: Introduction to Database Systems

20
 BI-A7/B2.2-R0: PERL PROGRAMMING AND APPLICATION TO BIOINFORMATICS

Objective of the Course

Perl is a popular programming language that is extensively used in Bioinformatics. The goal of this course
is to provide a practice-oriented introduction to Perl programming language. The goal is two-fold: to teach
programming skills and to apply them for the solution of interesting Bioinformatics problems. The
programming concepts such as data type, arithmetic and logical operators, conditionals and loops,
input/output, regular expression and pattern matching, functions and sub-routines, application in reading
protein files, finding motifs, simulating DNA, parsing PDB record, BLAST and annotations in GenBank,
etc. After completion of the course a student will have solid understanding of Perl basics and will be able
to program for tackling tasks described above.

Outlines of Course

S. No. Topics Minimum No. of hours

1. Introduction 02
2. Data Types 06
3. Arithmetic and Logical Operators 10
4. Conditionals and Loops 04
5. Input and Output 02
6. Regular Expression and Pattern Matching 12
7. Function and Subroutines 12
8. Applications of Perl in Bioinformatics 12
Lectures = 60
Practicals/ Tutorials = 60
Total = 120

Detailed Syllabus

1. Introduction: 2 hours

Introduction to Perl, Downloading and installation from Website, Writing and Running a Perl
Program, Editing, Advantages

2. Data Types 6 hours

Scalar data and scalar variables: Number, String, Conversion between Numbers and Strings,
Variable Interpolation, Arithmetic and Decimal Precision, Arrays: Initialization, Manipulation of
Array elements; Associative Array (Hashes): Initialization, Manipulation of Elements of Array.

3. Arithmetic and Logical Operators 10 hours

Arithmetic Operators, Assignment Operators, Increment and Decrement Operators, String
Concatenation and Repetition, Operators precedence and Associativity, Conditional Operators,
Logical Operators, Operators for manipulating arrays, Operators for Manipulating hashes.

4. Conditionals and Loops 4 hours

Conditional Statement; if, if…else, if and if-else, unless statement, Loops: while, for, until,
do..while, do..until and foreach loop, last next, redo, continue and case switch statement.

5. Input and Output 2 hours

Creating a file, Reading Data from a file, Writing data to a file, Closing a file, Managing Files and
Directories

21
6. Regular Expressions and Pattern Matching 12 hours
Regular Expression, Pattern Matching, Meta Character, Simple Pattern, Matching Group of
Characters, Matching multiple instances of Characters, Pattern Building, Pattern and Variable,
Pattern and Loops, Using Pattern for Search and Replace, Matching Pattern over multiple Lines
etc.

7. Function and Subroutines 12 hours

Built-in Functions, Defining and calling subroutines, Returning Values from Subroutines, Using
Local Variables in Subroutines, Passing Values into Subroutine, Perl References, Perl module
and their uses.

8. Applications of Perl in Bioinformatics 12 hours

Concatenating DNA Fragments, Transcription: DNA to RNA, Reading Protein Files, Finding
Motifs, Simulating DNA, Generating Random DNA, Analysing DNA, Translating DNA to Proteins,
Reading DNA from Files in FASTA format, Separating Sequence and Annotation, Parsing
Annotation, Parsing PDB files, Parsing BLAST output, Bio-perl .

RECOMMENDED BOOKS

MAIN READING

1. James Tisdall, “Beginning Perl for Bioinformatics”, O’Reilly & Associates, 2001
2. James Tisdall, “Mastering Perl for Bioinformatics”, O’Reilly, 2003

SUPPLEMENTARY BOOKS

1. Cynthia Gibas & Per Jambeck, “Developing Bioinformatics Computer Skills”, O’Reilly &
Associates, 2000.
2. Rex A. Dawyer, “Genomic Perl”, Cambridge University Press
rd
3. Learning Perl, 3 Edition , Author: Randal L. Schwartz and Tom Phoenix, O’Reilly

22
 BI-A7/B2.2-R0: PYTHON PROGRAMMING AND APPLICATIONS TO BIOINFORMATICS

Objective of the Course

The course is designed for students who already have some programming knowledge, in other languages
such as Perl or C. This course focus on bioinformatics application and examples and also covers the
necessary programming features of Python. Students who undertakes this course will be able to write
codes for simple applications and will motivate to develop modules for some specialized applications.

Outlines of Course

S. No. Topics Minimum No. of hours

1. Introduction to Python 6
2. Syntax rules 6
3. Variables and namespaces 4
4. Control flow 4
5. Functions 6
6. Exceptions 4
7. Modules and Packages 4
8. Classes 6
9. Biopython 10
10. Biopython – applications 10
Lectures = 60
Practicals/ Tutorials = 60
Total = 120

Detailed Syllabus

1. Introduction to Python 6 hours

Basic data types – Strings, Lists, Tuples – Lists and Tuples – Strings and Unicode strings
Buffers – Dictionaries – Numbers – Type conversions – Files

2. Syntax rules 6 hours

Indentation – Line structure – Block structure – Special objects

3. Variables and namespaces 4 hours

Variables – Multiple assignments – Assignments, references and copies of objects –

Namespaces – Accessing namespaces

4. Control flow 4 hours

Conditionals – Loops – while – for – more about loops

5. Functions 6 hours

Operators – Order of evaluation – Object comparisons – dot operator – String formatting –

Defining functions – Passing arguments to parameters – Reference arguments – Passing
arguments by keywords – Default values of parameters – Variable number of parameters

23
6. Exceptions 4 hours

General Mechanism – Python built-in exceptions – Raising exceptions – Defining exceptions

7. Modules and packages 4 hours

Modules – Loading – Packages – Loading

8. Classes 6 hours

Creating instances – Getting information on a class

9. Biopython 10 hours

Introduction – Bio.Seq and Bio.SeqRecord modules – Using Seq class – Sequences reading and
writing – Bio classes for sequences – Bio.SwissProt.SProt and Bio.WWW.ExPASy – Reading
entries – Regular expressions in Python – Prosite - Bio.GenBank – Reading entries – Running
Blast and Clustalw – Blast - Clustalw - Running other bioinformatics programs under Pise

10. Biopython – applications 10 hours

Advanced Parsers – Introduction – building parsing classes for Enzyme – Iterator using the
parsers classes – Building parsing classes for phylogenetic trees working with PDB – Study of
disulfide bonds – Graphics in Python.

RECOMMENDED BOOKS

MAIN READING

1. Mark Lutz, David Ascher (2003) Learning Python. O’Reilly & Associates
2. Alan Gauld (2000) Learn To program Using Python Addison –Wesley

ADDITIONAL READING

1. AlexMartelli (2003) Python in a Nutshell, O’Reilly

RESOURCES

1. URL : http://www.python.org
2. URL : http://www.biopython.org

24
 BI-A8/B2.3-R0: INTRODUCTION TO OBJECT ORIENTED PROGRAMMING THROUGH JAVA

Objective of the Course

The course is designed to impart knowledge and skills required to solve the real world problems using
object – oriented approach utilizing JAVA language constructs. This course covers the subject in two
parts, viz., Java Language and Java Library.

After completion of the course students are expected to understand the following:

• Java tokens for creating expressions and creating Datatypes

• The way various expressions and data types are assembled in packages
• Implementation of Inheritance, Exception handling and Multithreading in JAVA.
• JAVA I/O basics and Applets
• Setting up GUI using AWT/Swing
• Network Programming in JAVA
• Accessing relational databases from JAVA programs

Outlines of Course

S. No. Topics Minimum No. of hours

1. The JAVA Language 30
2. The JAVA Library 30
Lectures = 60
Practicals/ Tutorials = 60
Total = 120

Detailed Syllabus

1. The JAVA Language 30 hours

1.1 Introduction to JAVA 02 hours

An Overview of JAVA, JAVA Applets and Applications.

Difference between Java Script and JAVA
Object Oriented Programming features

1.2 Data Types, Variable & Arrays 03 hours

Java Token & Keywords. Integers types. Floating point types

The JAVA class libraries, Declaring a variable, Dynamic initialization, The scope and lifetime of
variable. Type conversion and casting.

Arrays: One-dimensional arrays, Multidimensional arrays, Alternative array declaration syntax

1.3 Operators 02 hours

Arithmetic operators, The Bitwise operators, Relational operators, Boolean logical operators, the
assignment operator, The ? Operator, Operator precedence

25
1.4 Control statements 03 hours

Selection statements, Iteration statements, Jump Statements

1.5 Introduction classes and objects 04 hours

Class fundamentals, Declaring objects, Assigning object reference variables, Introducing

methods, Constructors, The this keyboard, Garbage collection, The Finalize () method, a stack
class, Overloading constructors, Using objects as parameters, Arguments passing, Returning
objects, Recursion.

1.6 Inheritance 04 hours

Inheritance basics, Member access and inheritance, Using super class, Creating a multilevel
hierarchy, Method overriding, Dynamic method dispatch, Using abstract classes, Using final with
inheritance, The object class

1.7 Packages and Interfaces 03 hours

Packages ; Defining a package, Understanding classpath, Importing Packages

Interfaces : Defining an interface, Implementing interfaces, Applying Interfaces, Variable in
interfaces

1.8 Exception handling 03 hours

Exception handling fundamentals

Exception types: Uncaught exceptions. Using try and catch
JAVA’s build-in exceptions. User defined exception subclasses

1.9 Multithreaded Programming 03 hours

The JAVA thread model. The main thread, Creating a thread, Alive () and joint (), Suspend() and
resume (), Thread priorities, Synchronization, Interthread communication

1.10 I/O, Applets and Other Topics 03 hours

I/O Basics: Streams, The stream classes, The predefined streams, Reading console input,
Writing console output, Reading and writing files, Applet fundamentals, The transient and volatile
modifiers, Using instance of native methods

2. The JAVA Library 30 hours

2.1 String handling 02 hours

The string constructor, Special string operations, Character extraction, String Searching &
Comparison, Data conversion using value of (), String buffer

2.2 Exploring JAVA Lang 03 hours

Simple type wrappers, Runtime Memory management, Array copy, Object, Clone() and the
cloneable interface, Class & Class loader

Math functions: Transcendental functions, Exponential functions, Rounding functions,

Miscellaneous math methods

Compiler, Thread, Threadgroup and runnable, throwable, Security Manager

26
2.3 The utility classes 03 hours

The enumeration interface, Vector & Stack

Dictionary. Hash table, String tokenizer,
Bitset. Date: Date comparison, String and time zones
Random. Observer interface

2.4 Input/Output – Exploring JAVA I/O 03 hours

The JAVA I/O classes and interface

File Namefilter and Directories
I/O Stream classes: File Input Stream, File Output Stream, Byte array input stream, Byte array
output stream, Filtered streams
Buffered Streams: Buffered Input Stream, Buffered Output Stream, Push back Input Stream,
Sequence Input Stream, Print Stream, Random Access File

2.5 Networking 04 hours

Socket Overview, Reserved sockets, Proxy Servers

Internet Addressing: Domain naming services (DNS), JAVA and the net, The networking classes
and interfaces, Inet Address: Factory methods, Introspection, TCP/IP server sockets
DataGrams: Datagram packet, Datagram server and client

2.6 The applet class 05 hours

The applet class, Applet architecture

An applet skeleton: Initialization and termination, Overriding update (), Status Window
Handling events: The event class, Processing mouse events
Handling keyboard events
HTML applet.tag, Passing parameters to applets
Applet context and show document (), The audioclip & appletstub interface, Outputting to the
console

2.7 Swing 05 hours

Swing & its features

Text fields, Buttons, Toggle Buttons, Check boxes, and Radio Buttons, Viewports, Scrolling,
Sliders and Lists, Combo Boxes, Progress Bars, Tooltips, Separators and Choosers, Layered
Panes, Tabbed Panes, Split Panes and Layouts, Menus and Toolbars, Windows, Desktop
Panes, Inner Frames, Dialogue Boxes, Tables and Trees, Text Components

2.8 Images 02 hours

File Formats
Image Fundamentals: Creating, Loading and Siaplaying
Image Observer: Double Buffering, Media Tracker

2.9 JAVA Database Connectivity (JDBC) 03 hours

Introduction to JDBC. Type of JDBC connectivity

Accessing relational database from Java programs
Establishing database connections

27
RECOMMENDED BOOKS

MAIN READING

1. H. Schildt, (2001), “The Complete Reference – Java 2”, Fourth Edition, Tata McGraw Hill
2. Dietel nad Dietel (2001), “Java: How to program Java 2”, Second Edition, Pearson Education

SUPPLEMENTARY READING

1. D. Hanagan (2001), “Java Examples in a Nutshell”, Third Edition, O’ Reilly

2. K. Mughal and R. W. Rasmuessen, “A Programmers Guide to Java Certification – First Edition,
(1999), Pearson Education Comprehensive Primer” publication
3. M. T. Nelson, “ Java Foundation Classes”, Tata McGraw Hill

BI-A9/B2.4-R0 : ELEMENTS OF PROTEIN SEQUENCE, STRUCTURE & MODELLING

Objective of the Course

The course is formulated keeping in view first year Bachelor’s students with no biology
background. The essential focus is on a qualitative and elementary exposition of the idea that
proteins are important biological polymer molecules made of amino acid units, that proteins
possess unique structures which in turn dictate their function inside the cell and that it is
possible to store, retrieve and represent this information on computers. Other biological
macromolecules are introduced towards the end of the course. After attending the course, the
student is expected to be acquainted with protein sequences, structures and their role inside the
cells, their relation to diseases and drug targets, and how computers may help in understanding
structure and function of proteins.

Outline of Course

S. No. Topic Minimum No. of Hrs.

1. Protein Sequences & Structure 10
2. Ramachandran Plots 03
3. Protein databases & visualization 07
4. Structure to function relationships 05
5. Homology modeling of proteins 07
6. Protein conformation 06
7. Experimental techniques for proteins 04
8. Introductory Proteomics 02
9. Proteins as drug targets 06
10. Structure and function of Nucleic acids, lipids & 10
carbohydrates

Lectures = 60
Practicals/Tutorials = 60
Total = 120

28
 Detailed Syllabus

1. Protein Sequences & Structure 10 hrs.

a> Building Blocks : Amino acids and their classification, peptide bond, polypeptides,
proteins.
b> Primary structure – protein sequence.
c> Secondary structures : alpha helix, beta sheet (parallel & antiparallel), loops and
turns.
d> Tertiary structure
e> Quarternary structure (more than one polypeptide chain)
f> Classification of protein structures

2. Ramachandran Plots 3 hrs.

a> Glycine
b> Alanine
c> An example of any polypeptide
3. Protein databases & visualization 7 hrs.
a> Protein databases :
i) Sequence databases : NCBI, TIGR, SWISS-PROT
ii) Structure database : RCSB (and links therein)
iii) Other databases of conserved domains, motifs, protein families, etc.
b> Sequence retrieval : web browsing, ftp
c> Structure retrieval and visualization of 3D structures using Rasmol and other
public domain software.
4. Structure to function relationships 5 hrs
Sequence to function and Structure to function relationships -
a> Some case studies
5. Homology modeling of proteins 7 hrs.
Basic Concepts in modeling of proteins through homology
a> Sequence alignment
b> Coordinate assignment
c> Prediction of protein structure
d> Physico-chemical interactions in proteins in aqueous media
6. Protein conformation 6 hrs.
a> Active forms & Zymogens
b> Denaturation and renaturation, effect of salts, solvents & temperature.
c> Protein misfolding and protein aggregation
7. Experimental techniques for proteins 4 hrs.
a> Basic principles of amino acid sequencing

29
 b> Protein synthesis
c> Isolation, purification, characterization & estimation
8. Introductory Proteomics 2 hrs.
Proteomics : Comparative genome analysis using proteomics –
Differential expression on 2D- gel
9. Protein as drug targets 6 hrs.
Some case studies
10. Structure and function of Nucleic acid, lipids & carbohydrates 10 hrs.
Introduction to Nucleic acids, lipids & carbohydrates.

RECOMMENDED BOOKS

MAIN READING

1. C, Branden & C. Tooze, “Introduction to Protein Structure”, Garland Publishing Inc., New
York, 1991.
2. T.E. Creighton, “Proteins – Structures and Molecular Properties”, W.H. Freeman & Co.,
New York, 1993.

SUPPLIMENTARY BOOKS

1. EE Conn & PK Stumpf, “Outlines of Biochemistry”, Wiley Eastern.

2. R.R. Sinden, “DNA Structure and Function”, Academic Press, San Diego, 1994.
3. Bioinformatics Sequence, Structure and Databanks Edited by D. Hidggins & W. Taylor,
Oxford University Press, 2000.

30
 BI-A10/B2.5-R0 : BASICS OF GENOMICS AND PROTEOMICS

Objective of the Course

The primary objective of this course is to impart advanced knowledge to students on a self
learning mode such that students become familiar with the methods of searching for information
and analyzing preliminary data.
After completion of this course the student should be able to
• Understand state-of-the-art molecular biology techniques
• Be conceptually familiar with metabolism
• Interpret preliminary gene expression and protein expression studies
• Be familiar with the various genome projects completed and ongoing

Outline of Course

S. No. Topic Minimum No. of hrs.

1. Advanced Biochemistry 10
2. Metabolism and Pathways 8
3. Basic concepts in Genomics 10
4. Micro array for gene expression 10
5. Proteomics 10
6. Genome Projects – The unfolding story 12

Lectures = 60
Practicals / Tutorials = 60
Total = 120

Detailed Syllabus

1. Advanced Biochemistry 10 hrs

An introduction to physical biochemistry, intermediary metabolism and molecular biology.
Topics include a survey of structure, chemistry and function of proteins and nucleic acids;
regulation of gene expression at the level of DNA, RNA, and protein synthesis.
2. Metabolism and Pathways 8 hrs.
Pathways of carbohydrate, lipid and nitrogen metabolism and their metabolic control.
3. Basic concepts in Genomics 10 hrs.
Whole genome analysis, Genome sequencing technology.
Comparative genomics – Paralogs and orthologs, Phylogeny, Human genetic disorders,
Candidate gene identification, Concepts of Pharmacogenomics.

31
4. Micro array for gene expression 10 hrs.
Target selection, customized microarray design, image processing and quantification,
normalization and filtering, statistical analysis, public microarray data sources.
5. Proteomics 10 hrs.
Basics of Protein structure, Introduction to basic Proteomics technology, Bio-informatics in
Proteomics, Basics of Proteome Analysis, Concepts in Enzyme Catalysis.
6. Genome Project – The unfolding story 12 hrs.
Introduction to the concepts cloning and mapping, Construction of Physical maps, Basics
of radiation hybrid maps, Sequencing : Related discoveries and technology development,
Implications of the Human Genome Project, Basic Human Inheritance Patterns, Basics of
Single Nucleotide Polymorphism detection and its implication, Practical Application of
medical Genetics Technology.

RECOMMENDED BOOKS

MAIN READING

1. Genomes. Author : T.A. Brown, John Wiley and Sons, Bios Scientific Publishers
2. Discovering Genomics, Proteomics and Bioinformatics Campbell AM and Heyer LJ
Perason Education (Low priced Editions) 2003.

SUPPLIMENTARY BOOKS

1. Principles of Genome Analysis and Genomics (Third Edition) Primrose and Twyman
Blackwell publishing (2003)
2. Reiner Westermeier and Tom Naven. Proteomics in practice. Wiley-vch. 3rd Edition 2002
3. Instant Notes-Bioinformatics Authors : D.R. Westheadn, J.H. Parish and R.M.Twyman.
Publisher : Viva Books Pvt. Ltd. IndianEdition 2003.

32
SEMESTER – III

33
 BI-B3.1-R0 : COMPUTER ORGANIZATION AND DISTRIBUTED SYSTEMS

Objective of the Course

Objective of the course is to familiarize students about computer hardware design and
distributed systems, basic structure and behavior of the various functional modules of the
computer and how they interact to provide the processing needs of the user.

This subject mainly focuses on the computer fundamentals, network and distributed systems,
architectural models, fundamental models, networking and internetworking, operating systems &
its supports for distributed systems. Students will be exposed to internet principles, different
types of networking topologies. OSI (Open System Interconnection) seven layer model. The
course also deals in memory management, methodologies for enhancement of processor
throughout besides process control and interprocess communication.

Outline of Course

S. No. Topic Minimum No. of hrs.

1. Fundamentals 11
2. Basic Computer Organization 12
3. Introduction to Networks and Distributed Systems 5
4. Distributed Systems Models 6
5. Networking and Internetworking 6
6. Interprocess Communication 6
7. Operating Systems & its supports for DS 14

Lectures = 60
Practicals / Tutorials = 60
Total = 120

Detailed Syllabus

1. Fundamentals 11 hrs.
Binary number systems, Two’s complement, floating point representation, addition,
subtraction,overflow.
Logic gates, flip-flops, encoders, decoders, multiplexers, registers, counters, RAM, ROM.

2. Basic Computer Organization 12 hrs.

Bus and Memory transfers, Binary adder, counter, arithmetic circuit, Logical and shift
operations Instruction codes, direct and indirect addressing, Instruction cycle, Instruction
formats such as one address and two address instructions, memory reference instructions,
input output instructions, arithmetic, logical and shift instructions, general register
organization, Memory stack, brief introduction to interrupts.

34
3. Introduction to Networks and Distributed Systems 5 hrs.
The motivation and goals of network and distributed system, network topologies, layers in
a network, OSI (Open Systems interconnection) seven layer model (introduction, e.g.,
Chapter 1 of Tanenbaum), characteristics of a distributed computing system, issues such
as heterogeneity, openness, security, scalability, concurrency.

4. Distributed Systems Models 6 hrs.

Architectural Models : client server model, peer processes model, mobile agents, thin
clients, spontaneous networking, issues in designing distributed systems,
Fundamental models : interaction model, failure model, security model and related issues.

5. Networking and Internetworking 6 hrs.

Networking issues, types of networks – local area networks, wide area networks,
metropolitan area networks, wireless network and internetwork. Networks principles –
protocols, routing, packet transmission, data streaming, switching schemes. TCP/IP
protocols – IP addressing, IP routing, mobile IP.

6. Interprocess Communication 6 hrs.

Characteristics of interproces communication, sockets, UDP datagram communication,
TCP stream communication, external data representation and marshalling. Client-server
communication – the request-reply protocol and related issues, use of TCP streams to
realize request-reply protocol. Group communication, use of IP-multicast to implement
group communication.

7. Operating Systems & its supports for DS 14 hrs.

Tasks of OS, types of OS, OS structure.
Programs and process, process control, interacting processes, synchronization,
interprocess communication,
Fork-Join primitives, parbegin-Parend control structure, Threads and their creation and
termination, kernel levels threads, user level threads. – (chapters 9 and 10 of Dhamdhere).
Memory management – Memory allocation model, contiguous memory allocation and
related issues, non-contiguous memory allocation – virtual memory management through
demand paging – (15 of Dhamdhere).
Enhancement of throughput by multi-threading, architectures for multi-threaded servers,
threads versus multiple processes, OS supports for communication and invocation,
concurrent invocation, asynchronous invocation, desirable architecture of OS for
distributed computing – (chapter 6 of Coulouris, Dollimore & Kindberg).

35
RECOMMENDED BOOKS

MAIN READING

1. George Coluouris Jean Dollimore Tim Kindberg, Distributed Systems : Concepts and
Design, Pearson Education, 2001.

2. M.M. Mano : Computer Systems Architecture, 3rd Edition, Pearson Education, 2000.

3. D.M. Dhamdhere, Systems Programming and Operating Systems, Tata McGraw Hill,
1996.

4. A. Tannenbaum & Van Steen, Distributed Systems Principles and Paradigms, 1st Edition,
2002 Prentice Hall

SUPPLEMENTARY READING

1. H.F. Korth and A. Siberschatz : Database System Concepts, McGraw Hill.

2. J.P. Hayes : Computer Architecture and Organization, McGraw-Hill.

3. John D. Carpinelli, Computer Systems Organization & Architecture Pearson Low priced
Edition 2004.

36
 BI-B3.2-R0 : PROBABILITY AND INFORMATION THEORY

Objective of the Course

Biological processes are inherently random. A rational description would require study of
probabilistic framework. Analysis of vast amount of biological data sets would require a through
understanding of probability theory. For quantifying uncertainty embedded in a biological system,
tools from information theory are useful. For simulating biological phenomena, Monte Carlo methods
are generally employed. This course will provide foundational support to the field of Bioinformatics.
Outline of Course

S. No. Topic Minimum No. of hrs.

1. Introduction to Probability Theory 4
2. Random Variables 12
3. Conditional Probability and Expectation 4
4. Limit Theorems 4
5. Elements of Stochastic process and Markov Chains 10
6. Information Theory 8
7. Information source :Memoryless, and with memory 8
8. Monte Carlo methods 10

Lectures = 60
Practicals / Tutorials = 60
Total = 120

Detailed Syllabus

1. Introduction to Probability Theory 4 hrs.

Probability defined on events, Conditional Probability, Bayes’ theorem

2. 12 hrs.
a> Random Variables
Discrete Random variables : - Bernoulli, Binomial, Geometric and Poisson
distributions.
Continuous Random variables : - Uniform, Exponential, Normal, Gamma, and Chi-
square distributions.
Expectation of random variables.
Chebyshev’s inequality.
Jointly distributed random variables.
b> Functions of Random Variables
Minimum, Maximum sum of Random Variables

3. Conditional Probability and Expectation 4 hrs.

37
 Discrete case, Continuous case, Computing Expectation by conditioning, Computing
probabilities by conditioning.

4. Limit Theorems 4 hrs.

Weak law of large number.
The Central Limit Theorem.
The Strong Law of Large Numbers.

5. Elements of Stochastic processes and Markov Chains 10 hrs.

Introduction to stochastic processes.
How to characterize a stochastic process?
Markov processes and Markov chains.
Chapman – Kolmogorov equation.
Classification of states.
Limiting probabilities.

6. Information Theory 8 hrs.

What is Information?
Surprise and Uncertainty.
Shannon’s Information measure.
Conditional, Joint and Mutual Information measure.
Kullback-Leibler Directed Divergnce.
The communication model

7. a) Discrete memory-less Information source 8 hrs.

The discrete information source.
Source coding.

b) Discrete Information source with memory

Markov Chain.
State transition diagram.
Amount of information in a first order Markov chain.

8. Monte Carlo Methods 10 hrs.

Random number generator.
Linear Congruential Method
Techniques for generating continuous random variables.
- Inverse Transformation Method
Simulating from discrete distributions.
Variance reduction techniques.
Hit or Miss Monte Carlo method
- Approximate evaluation of
Note : Students have to familiarize with at least one statistical software like R for Linux,
SYSTAT/MINITAB

38
RECOMMENDED BOOKS

MAIN READING

1. S.M. Ross, “A First course to Probability”, 6th Edition, Pearson Education.

2. J.L. Devore, “Probability and Statistics”,Thomson, 2002.

3. J.C.A. Vander Lubbe, ”Information Theory”, Cambridge University Press, 1997.

SUPPLEMENTARY READING

1. W.J. Ewens and G.R. Grant, “Statistical methods in Bioinformatics” : Anintroduction,

Springer-Verlag 2001.

2. S.M. Ross, “Probability Models”, 7th Edition, Harcourt India Private Limited, 2001

3. D. Applebaum, “Probability and Information” – and integrated approach, Cambridge 1996.

BI-B3.3-R0 : COMPUTATIONAL METHODS IN BIOMOLECULAR SEQUENCE ANALYSIS

Objective of the Course

The aim of course is to introduce and impart skills to students about the computational tools and
techniques which are needed to analyze Primary DNA and Protein sequences. This will enable them
to understand the significance of Protein structure and function. Some of the major Computational
issues and solutions will be covered with suitable examples. Focus will be on introducing few well
known algorithms and methods which are widely used in analyzing sequence. Basic knowledge in
Mathematics and Statistics is prerequisite. Students who undertake this course will get the
necessary understanding, exposure and foundation to take up small or large scale software
Development projects in the area of Bioinformatics.
After the end of this module the students can :
1. Use and apply state of the art tools pertaining to Sequence analysis
2. Will be able to analyze primary DNA and Protein sequences and interpret results
3. Will have the understanding of the methodology or algorithm employed in sequence analysis
tools
4. Will be in a position to undertake software development project relate to sequence analysis
Outline of Course

S. No. Topic Minimum No. of hrs.

1. Basic concepts of Molecular Biology 6
2. Sequence composition and statistics 4
3. Strings, Graphs and algorithms 6
4. Pairwise and Multiple alignment 12

39
5. Database homology Search 10
6. Statistical Modeling of sequences 4
7. Pattern recognition and motif analysis 6
8. Secondary structure prediction 6
9. Phylogenetic analysis 6

Lectures = 60
Practicals / Tutorials = 60
Total = 120

Detailed Syllabus

Note : Appropriate References to Mainreading are suggested for teaching purpose.

1. Basic concepts of Molecular Biology [Refer MR-1] 6 hrs.

1.1 Proteins (1 hour)
1.2 Nucleic Acids (1 hour)
1.2.1 DNA
1.2.2 RNA
1.3 Molecular Genetics (4 hours)
1.3.1 Genes and Genetic code
1.3.2 Transcription, Translation and Protein synthesis
1.3.3 Chromosomes
1.3.4 Prokaryotic and Eukaryotic Gene structure

2. Sequence composition and statistics [SR-1] 4 hrs.

2.1 Nucleotide and amino acid compositions
2.2 Codon usage and statistics
2.3 AT and GC rich regions

3. Strings, Graphs and Algorithms [Refer MR-1] 6 hrs.

3.1 Strings (1 hour)
3.2 Graphs (2 hours)
3.3 Algorithms (3 hours)

4. Pairwise and Multiple alignment [Refer MR-1, 2 & 3 12 hrs.

4.1 Pairwise alignment (6 hours)
4.1.1 Global alignment
4.1.2 Local alignment
4.1.3 Scoring functions
4.1.4 General gap and affine gap penalty
4.1.5 Statistical significance

40
 4.2 Multiple Sequence alignment (6 hours)
4.2.1 SP (Sum of Pairs) measure
4.2.2 Star alignments
4.2.3 Tree alignments
4.2.4 Motifs and Profile
4.2.5 Alignment Representation and Applications
4.2.6 ClustalW, clustalX, Hmmer and T-cofee

5. Database homology search [Refer MR2 & SR-1, 4] 10 hrs.

5.1 Scoring matrices
5.2 BLAST algorithm
5.3 Significance of alignments (6 hours)
5.4 Blast versions : Blastp, Blastx, tBlastn, tbalstx
5.5 PSI and PHI Blast

6. Statistical Modeling of Sequence [MR-2] 4 hrs.

6.1 Independent and indentically distributed sequences
6.2 Markov Chain models

7. Pattern Recognition and Motif analysis 6 hrs.

7.1 Restriction site
7.2 Finding repeats
7.3 General Pattern search
7.4 DNA and Protein motifs search
Transfac
Prosite

8. Secondary structure Analysis [MR-3] 6 hrs.

8.1 Stem and Loop structure
8.2 RNA fold algorithm

9. Phylogenetic analysis [MR-1 and MR-3] 6 hrs.

9.1 Distances and Parsimony methods
9.2 Clustering methods
9.3 Rooted and Unrooted tree
9.4 Bootstrap analysis
9.5 PHYLIP

41
RECOMMENDED BOOKS

MAIN READING

1. Setubal Joao and Meidanis Joao, “Introduction to Computational Molecular Biology”, PWS
Publishing Company (An International Thomson Publishing Company), 1997, Indian low
priced edition.

2. Warren Ewens and Gregory R. Grant, “Statistical Methods in Bioinformatics : An

Introduction” Springer-Gerlag 2001.

3. R. Durbin, S. Eddy, A. Krogh and G. Mitchison, “Biological sequence analysis :

Probablistic models of proteins and nucleic acids”, Cambridge University Press, 1998
Indian low priced edition.

SUPPLEMENTARY READING

1. Mount “Bioinformatics” Cold Spring Harbor Laboratory.

2. Stephen A. Krawtz and David D. Womble “Introduction to Bioinformatics : a theoretical and

practical approach. Humana Press.

3. Neil C. Jones and Pavel A Pevzner. An introduction to Bioinformatics algorithms MIT

Press reprinted by Ane Books, New Delhi 2005.

4. Ian korf, Mark yandell & Joseph Bedell. “BLAST”. O’Reilly press 2003.

42
 BI-B3.4-R0 : DISCRETE MATHEMATICS

Objective of the Course

The objective is to provide the necessary mathematical knowledge so that students can understand
computational issues relating to practical problems. The paper intends to equip the students with the
necessary mathematical ideas, notations and techniques that are required to formulate an algorithm
for a problem, and to reason about its time and pace complexity. Many problems of bioinformatics
are combinatorial in nature. This course will help to solve such problems also.

Outline of Course

S. No. Topic Minimum No. of hrs.

1. Sets, graphs and trees 13
2. Counting and probability 9
3. Recurrences and generating functions 10
4. Boolean algebra 5
5. Graph algorithms 9
6. Modeling computation : grammer, language and 9
automata
7. NP-completeness 5

Lectures = 60
Practicals / Tutorials = 60
Total = 120

Detailed Syllabus

1. Sets, graphs and trees 13 hrs.

Sets, operations on sets, principle of inclusion and exclusion, countable and uncountable
sets, Cartesian product, n-ary relation, binary relation, operations on relations, reflexivity,
symmetry, transitivity, equivalence relation, equivalence class, partition, partial order,
composite of relations, closures of relations, Warshall’s algorithm for transitive closure.
Functions, domain, range, injection, surjection, bijection, composition of functions,growth of
functions – asymptotic q-notation, O-notation, W-notation, o-notation, w-notation and their
properties.
Simple graphs, multigraphs, directed graphs, undirected graphs, degree, reachability, paths,
cycles, isomorphism, bipartite graphs, trees, rooted trees, forest, k-ary trees, basic
properties of graphs and trees.

2. Counting and probability 9 hrs.

Summation and product rules, pigeonhole principle, permutation, combination, binomial
coefficients and related identities, sample space, discrete probability distribution, conditional
probability, independence, Baye’s theorem, Bernoulli’s trials, binomial distribution, simple
probabilistic reasoning such as birthday paradox.

43
3. Recurrences and generating functions 10 hours

Linear homogeneous recurrence relations, linear non-homogeneous recurrence relations, solving

recurrences by direct method, iteration method, master method, recurrence trees, generating
functions for a sequence, solving simple counting problems using generating functions, solving
recurrence relations using generating functions.

4. Boolean algebra 5 hours

Boolean expression and function, formal definition of Boolean algebra, identities, combinatorial
circuits, Karnaugh maps.

5. Graph algorithms 9 hours

Graph representation scheme, breadth first search, depth first search and their properties,
decomposing a directed graph into its strongly connected components, Euler tour, minimum
spanning tree, Prim’s algorithm, Kruskal’s algorithm, shortest path problem, Dijkstra’s algorithm
and Bellman –Ford Algorithm for single source shortest paths problem.

6. Modeling computation: grammar, language and automata 9 hours

Terminals, non-terminals, grammar, language, types of grammar – context sensitive and context
free grammar, parse tree, finite state automata, non-deterministic finite state automata, regular
expression, regular sets, Kleene’s theorem Turing machine.

7. NP-completeness 5 hours

Introduction to complexity class P, verification algorithm, complexity class NP, reduction function,
reduction algorithm, NP-completeness

RECOMMENDED BOOKS

MAIN READING

1. Introduction of Algorithms, T. Coreman, C. E. Leiserson, and R. L. Rivest

th
2. Discrete Mathematics and its Applications, Kenneth H. Rosen, McGraw Hill Companies, 4
Edition

44
SEMESTER – IV

45
 BI-B4.1-R0: STATISTICAL METHODS IN BIOINFORMATICS

Objective of the Course

Statistics as a discipline deals with collection and analysis of data. The collection of data involves
techniques of sampling methods while the analysis involves inferences and estimation based on sampled
data. In Bioinformatics the same principle regarding scientific data collection and analysis of data hold. To
investigate, large scale data sets generated from various genomes, proteome, metabolomic projects and
related sources, it is necessary to have a proper grounding in statistical techniques.

Outline of Course

Minimum No. of
S. No. Topic
Hours
1. Review 04
2. Sampling Distributions 05
3. Estimation Theory 08
4. Maximum Likelihood Esimation 04
5. Inference – Tests of Hypotheses 16
6. Simple Linear Regression and Correlation 06
7. Analysis of Variance 06
Statistical methods for Stochastic
8. 05
Processes
Statistical Analysis of Stochastic
9. 06
Processes
Lectures = 60
Practical / Tutorials = 60
Total = 120

Detailed Syllabus

1. Review 4 hours

Mean, Median, Mode

Standard Deviation, Variance and Correlation
(Emphasis to be placed on hands on approach with real data sets)
Probability limits and distribution theorems

2. Sampling Distributions 5 hours

Statistic
Distribution of sample mean
Sample variance – (application of Central limit theorem)

3. Estimation Theory 8 hours

Biased and unbiased estimator

Confidence interval: population mean, proportion
Variance

46
4. Maximum Likelihood Estimation 4 hours

Discrete and Continuous distributions

Likelihood function
Log-likelihood functions
(use of package recommended)
5. Inference – Test of hypotheses 16 hours
a) Formulation of Hypothesis ….4 hours
Simple and Composite
Type I and Type II errors
Power of a test
Significance of a test
P-value
b) Testing ….6 hours
Normal, Chi-Square, t-test and F-test
c) Chi-Square goodness of fit …..4 hours
Test of diversity based on entropic method
d) Non-parametric: Mann-Whitney test ….. 2 hours

6. Simple Linear Regression and Correlation 6 hours

Linear regression model

Least squares methods
Estimating model parameters
Residual sum of squares

7. Analysis of Variance 6 hours

Single factor ANOVA

Multi-comparison ANOVA

8. Statistical Methods for Stochastic Processes 5 hours

Testing of independence
Testing of Markov property
Association test

9. Analysis of Stochastic process 6 hours

Long Repeat
Scan Statistics
Analysis of Patterns

RECOMMENDED BOOKS

MAIN READING

1. W. J. Ewens and G. R. Grant, “Statistical Methods in Bioinformatics”: An introduction Springer-

Verlag 2001
2. J. L. Devore, “Probability and Statistics”, (Fifth Edition), Thomson Asia, 2002
th
3. S. M. Ross, “A First course to Probability”, 6 Edition, Pearson Education

47
 BI-B4.2-R0: BIOMOLECULAR STRUCTURE & DYNAMICS

Objective of the Course

This course is formulated keeping in view first year Master’s students with ‘A’ level (DOEACC)
background in biology. The focus is on imparting a sound knowledge of structure and dynamics of
proteins and nucleic acids and modelling them in silico. After attending the course, the students are
expected to handle research projects in biomolecular structure and function.

Outline of Course

Minimum No. of
S. No. Topic
Hours
Protein Structure, Classification of protein
Structure, Membrane proteins, Viral
1. 10
Proteins, Proteins in immune system,
Proteins as drug targets.
Manipulating protein structures on
computer, Cartesian and internal
2. coordinate representations , ribbon 10
diagrams, space filling models, topology
diagram, searching for sequences & folds
3. Nucleic acid structures – A review 10
Database analyses of internal degrees of
4. 5
freedom of nucleic acid structures
Forces stabilizing Protein & Nucleic Acid
5. 5
structures
Energy minimization and Molecular
6. 15
Dynamics methods
Structure and function of Carbohydrates
7. 5
and Lipids.
Lectures = 60
Practical / Tutorials = 60
Total = 120

Detailed Syllabus

1. a) Protein structure – A review of primary, secondary, tertiary and quaternary structures,

motifs and folds.
b) Classification of protein structures
c) Membrane proteins
d) Viral proteins
e) Proteins in immune system
f) Proteins as drug targets 10 hours

2. Manipulating protein structures on computer, Cartesian and internal coordinate representations,

ribbon diagrams, space filling models, topology diagrams, searching for sequences & folds.
10 hours

48
3. Nucleic acid structures – A review

a) Right handed (A, B) and left handed (Z) double helical DNA.
b) Structures of t-RNA and r-RNA
c) DNA bending
d) DNA supercoiling
e) Cruciforms, triplexes and quadruplexes
f) Nucleic acids as drug targets 10 hours

4. Database analyses of internal degrees of freedom of nucleic acid structures 5 hours

5. Forces stabilizing Protein & Nucleic Acid structures 5 hours

6. Energy minimization and Molecular Dynamics methods 5 hours

a) Theory
b) Application to Proteins 5 hours
c) Applications to nucleic acids 5 hours

7. Structure and function of Carbohydrates and Lipids 5 hours

RECOMMENDED BOOKS

MAIN READING

1. C. Branden & C. Tooze, “Introduction to Protein Structure”, Garland Publishing Inc. New York,
1991
2. R. R. Sinden, “DNA Structure & Function”, Academic Press, San Diego, 1994

SUPPLEMENTARY READING
th
1. Lehninger principles of Biochemistry, David Nelson and Michael M. Cox, Freeman Publishing, 4
Edition 2004
2. A. R. Leach, “Molecular Modelling – Principles & Applications” Addison Wesley Longman, Essex,
1996

49
 BI-B4.3-R0: DATA STRUCTURES AND ALGORITHMS

Preamble

“Data Structures and Algorithms” can be considered as a classic, core topic of computer science. Data
structures and algorithms are central to the development of good quality programs. Their study is very
critical for a sound understanding and efficient implementation of Bioinformatics algorithms and programs.

Objective of the Course

(1) To gain a sound understanding of different types of data structures and their role in algorithm
design in computer science (in general) and in bioinformatics (in particular).

(2) To be able to understand any typical algorithm design problem in computer science and
bioinformatics and be able to visualize appropriate data structures for efficiently implementing the
algorithm.

(3) To be able to prove why a particular data structure is best suited for a particular problem, by
analyzing the algorithm in a sound and systematic way.

Outline of course

Minimum No. of
S. No. Topic
Hours
1. Introduction 2
2. Computational Complexity 6
3. Essential Preliminaries 5
4. Dictionaries 12
5. Priority Queues 4
6. Graphs 12
7. Sorting Methods 6
8. String Matching 4
9. Algorithm Design Paradigms 9
Lectures = 60
Practical / Tutorials = 60
Total = 120

Detailed Syllabus

1. INTRODUCTION 2 hours

Abstract data type and data structures, Classes and objects

2. COMPUTATIONAL COMPLEXITY 6 hours

Complexity of algorithms: worst case, average case and amortized complexity, notation for
algorithm complexity, Algorithm analysis, Recurrence relations, Introduction to NP-completeness

50
3. ESSENTIAL PRELIMINARIES 5 hours

Overview of recursion, iteration, arrays, pointers, lists, stacks, queues

4. DICTIONARIES 12 hours

Dictionaries: Hash tables, Binary search trees, splay trees, Balanced Trees, AVL trees, 2-3 trees,
B-Trees

5. PRIORITY QUEUES 4 hours

Priority Queues : Heaps, binomial queues, Applications

6. GRAPHS 12 hours

Graphs: Shortest path algorithms (Dijkstra, Bellman-Ford, Floyd-Warshall), minimal spanning tree
algorithms (Prim, Kruskall), depth-first, breadth-first search, and their applications.

7. SORTING METHODS 6 hours

Sorting: sorting methods and their analysis (shell sort, quicksort, merge sort, heap sort, radix
sort), lower bound on complexity

8. String Matching 4 hours

String matching algorithms (Rabin-Karp, Knuth-Morris-Pratt)

9. ALGORITHM DESIGN PARADIGMS 9 hours

Algorithm Design Paradigms: Greedy methods, divide and conquer, dynamic programming,
backtracking, local search methods, branch and bound technique. Travelling salesman problem.

RECOMMENDED BOOKS

MAIN READING

1. A. V. Aho, J. E. Hopcroft, and J. D. Ullman, Data Structures and Algorithms, Addison Wesley,
Reading Massachusetts, USA, 1983 (Available in Indian Edition)

2. M. A. Weiss, Data Structures and Algorithms Analysis in C++, Benjamin / Cummins, Redwood
City, California, USA, 1994 (Available in Indian Edition)

SUPPLEMENTARY BOOKS

1. T. H. Cormen, C. E. Leiserson, and R. L. Rivest, Introduction to Algorithms, the MIT Press,

Cambridge, Massachusetts, USA, 1990 (Available in Indian Edition)

2. Y. Narahari, Web-based Lecture Notes on Data Structures and Algorithms.

http://www.csa.iisc.ernet.in/~hari

51
 BI-B4.4-R0: COMPUTATIONAL GENOMICS

Objective of the course

Computational approaches are adopted right from Genome sequencing to sequence characterization.
This course module will provide the necessary basics and overview of the computational issues related to
Genomics. Application of in silico methods to some of the complex biological problems such as
Eukaryotic gene finding will be highlighted. Relevant and popular software tools and techniques employed
in this domain will be covered with suitable examples. Students at the end of the course will be able to
undertake pilot software project in related topics.

Outline of Course

S. No. Topic Minimum No. of Hours

1. Prokaryotic and Eukaryotic Genomes 6
2. Sequencing methods and technologies 4
3. Computational methods in sequencing 8
Computational approaches for Gene
4. 6
Identification
5. Computational methods for gene prediction 12
6. Analysis of regulatory regions 6
7. Genome Characterization 6
8. Comparative genomes 6
9. Overview of Functional Genomics 6
Lectures = 60
Practical / Tutorials = 60
Total = 120

Detailed Syllabus

1. Prokaryotic and Eukaryotic Genomes 6 hours

Central Dogma of molecular biology

Prokaryotic Gene structure
Eukaryotic Gene structure
Genome Organization
Genome Databases

2. Sequencing methods and technologies 4 hours

Short-gun sequencing
Clone by Clone approach
Genome markers and maps

3. Computational methods in sequencing 8 hours

Sequencing errors
Base calling
Fragment assembly
Overlap and layout consensus

4. Computational approaches for Gene identification 6 hours

Signal based methods

Content based methods

52
 Homology based methods
Performance measures

5. Computational methods for gene prediction 12 hours

Statistical methods
Compositional bias
Non-randomness
Machine learning and probabilistic methods
Artificial Neural Network
Markov Chain
Hidden Markov Model

6. Analysis of regulatory regions 6 hours

Signals and Patterns

Promoter prediction
Transcription factor binding sites

7. Genome Characterization 6 hours

EST comparison
Blast analysis

8. Comparative genomes 6 hours

Gene order
Horizontal gene transfer
Transposable elements
Clusters of orthologus genes

9. Overview of Functional Genomics 6 hours

Repeats and diseases

Gene expression
Applications

RECOMMENDED BOOKS

MAIN READING

1. Mount (2001), “Bioinformatics : Sequence and Genome analysis”, Cold Spring Harbor Laboratory
press

2. Michael Waterman (1995), “Introduction to Computational Biology: Maps, Sequences and

Genomes”

3. Warren Ewens and Gregory R. Grant, “Statistical Methods in Bioinformatics : An introduction”,

Springer-Verlag 2001

4. Cecillia saccone and Grazianio pesole, Handbook of comparative Genomics. Principles and
methodology

SUPPLEMENTARY READING

53
1. R. Durbin, S. Eddy, A Krogh and G. Mitchison, “Biological sequence analysis: Probabilistic
models of proteins and nucleic acids”, Cambridge University Press, 1998

2. Thomas Lengauer (editor)”Bioinformatics – from Genomes to drugs”, Volume 1 “Basic

Technologies” Wiley – Vch Germany

3. Tao Jiang, Ying Xu and Michael Q. Zhnag (Editors) Current topics in computational Molecular
biology. Ane Books, New Delhi 2004 .

4. Pierre Baldi and Soren Brunak (2003) “Bioinformatics: The machine learning approach”, East
West Press, Low priced Edition, Delhi

SEMESTER – V

54
 BI-B5.1-R0 ; OPTIMIZATION, MACHINE LEARNING AND COMPUTATIONAL INTELLIGENCE

Objective of the Course

To provide the basic concepts and terminology of machine learning and to give an overview on the main
approaches to machine learning along with an understanding of the differences, advantages and
problems of the various approaches. On completion of the course students should be able to understand
and apply various clustering and classification algorithms in classical and computational intelligence
framework for bioinformatic problems. The intention is to provide the necessary theoretical background
also so that they can avoid blind use of such tools for practical problems. It is a self-contained course
which will also equip the students with the necessary knowledge of optimization theory.

Outline of Course

S. No. Topic Minimum No. of Hours

1. Optimization techniques 12
2. Genetic algorithms 7
3. Basic concepts of machine learning 5
4. Clustering and classification 14
5. Introduction to neural networks 3
6. Feed forward neural networks 12
Self-organizing maps and recurrent neural
7. 7
networks
Lectures = 60
Practicals/Tutorials = 60
Total = 120

Detailed Syllabus

1. Optimization techniques 12 hours

Concepts of local and global optimum, constrained and unconstrained optimization, gradient,
Hessian of a function, first order and second order necessary conditions for local minimizers,
method of steepest descent, steepest descent for quadratic function, Newton’s method,
Levenberg-Marquardt algorithm, and Lagrange multipliers methods.

2. Genetic algorithms 7 hours

Introduction to Genetic algorithms, exploitation and exploration, general structure of the basic
genetic algorithm, different coding schemes, fitness function, chromosome, population, basic
genetic operators, different selection mechanism, mutation, single point and multi-point
crossover, termination criteria, elitist strategy.

3. Basic concepts of machine learning 5 hours

Basic notions of learning,, introduction to learning algorithms, incremental learning, supervised

learning, unsupervised learning, reinforcement learning, instance based learning and analytical
learning.

4. Clustering and classification 14 hours

Introduction to clustering, maximum likelihood decomposition and its application to normal

mixtures, k-means clustering algorithms, hierarchical clustering algorithms.

55
 Introduction to classifier design, linear discriminant analysis – two category and multi category
cases, perceptron criterion and its minimization, decision trees (ID3, C4.5), impurity functions,
pruning methods, rule extraction from decision trees, nearest neighbour classifier, k-nearest
neighbour classifier, Bayes decision rule, lose function, minimum error rate classification, Bayes
classifier with multivariate normal density.

5. Introduction to neural networks 3 hours

Introduction to neural networks, introduction to biological neural network, motivation for artificial
neural network (ANN), significance of massive parallelism and characteristics of (ANN), various
types of architectures.

6. Feed forward neural network 12 hours

Layered networks, perceptron and motivation for multilayered perceptron (MLP), back-
propagation learning , use of Levenberg-Marquardt method in training of MLP’s, online vas batch
learning, issues relating to initialization, termination, choice of architecture. Radial basis function
networks and related training issues, properties of MLP and RBF.

7. Self-organizing maps and Recurrent neural networks 7 hours

Self-organizing feature map, recurrent neural networks, Hopfield network and its applications,
simulated annealing.

RECOMMENDED BOOKS

MAIN READING

1. R. O. Duda, P. E. Hart and D. G. Stork, Pattern classification, John Wiley Sons, Second Edition,
2000

2. D. E. Goldberg, Genetic algorithms in search, optimization and machine learning, Pearson

Education (Paper back)

3. Christopher M. Bishop, Neural Networks for Pattern Recognition, Oxford University Press, 1995

4. E. K. P. Chong and S. H. Zak, An introduction to optimization, John Wiley & Sons, 2001

5. Tom Mitchell, Machine Learning, McGraw Hill, 1997

ADDITIONAL BOOKS

1. J. T. Touand R. C. Ganzales : Pattern Recognition Principles, Addison-Wesley, 1977, W. I.

Zangwill: Non-linear Programming, Prentice Hall, 1969

2. P. E. Gill, W. Murray and M. H. Wright, Practical optimization, Academic Press, 1982

3. S. Haykin, Neural networks – a comprehensive foundation, Prentice Hall, 1998 Vojislav Kecman,
Learning and soft computing, Pearson Low priced Edition 2004

56
 BI-B5.2-R0 : OBJECT TECHNOLOGY FOR BIOINFORMATICS

Preamble

Object technology has emerged as a sound paradigm for modelling, analysis, design, and implementation
of complex software intensive systems. Object technology is indeed an attractive methodology to use in
Bioinformatics in the areas of software modelling, software design and database design. Emerging
software technologies such as component technology and distributed object technology, which are quire
important for Bioinformatics are all founded on the object oriented paradigm. What “Data Structures and
Algorithms” is to Bioinformatics programming, “Object Oriented Modelling and Design” is to Bioinformatics
software development.

Objective of the course

The objective of the course is to provide a sound technical exposure to the concepts, principles, methods,
and best practices in object oriented modelling and design as applied to Bioinformatics.

The version of the course is to produce “Object Technologists” with sound knowledge and superior
competence in building robust, scalable, and reliable software intensive systems in Bioinformatics. They
would have a clear appreciation of the role of abstraction, modelling and design patterns in the
development of a Bioinformatics product. They would be able to make optimal design choices and employ
the most relevant methods, best practices, and technologies for building a software intensive
bioinformatics product, regardless of its complexity and scale.

Outline of Course

S. No. Topic Minimum No. of Hours

1. Introduction to Object Technology 10
2. Unified Modelling Language (UML) 10
3. Object Oriented Modelling 10
4. Object Oriented Design 10
5. Distributed Objects and Component Technology 10
6. Object Oriented Databases 10
Lectures = 60
Practical / Tutorials = 60
Total = 120

Detailed Syllabus

1. INTRODUCTION TO OBJECT TECHNOLOGY 10 hours

Meaning of the following terms: model, notation, method, methodology, analysis, design, process
with examples, Evolution of object technology, difference between structured methodology and
OO methodology

Object characteristics: abstraction, encapsulation, modularity, hierarchy (aggregation,

composition, inheritance), polymorphism, concurrency, typing, persistence. Software
development process, Rational unified process.

57
2. UNIFIED MODELING LANGUAGE (UML) 10 hours

Need for UML. UML Diagrams: Class diagrams, object diagrams, use case diagrams, component
diagrams, deployment diagrams, state chart diagrams, activity diagrams, sequence diagrams,
collaboration diagrams, other essential UML features. Examples and case studies

3. OBJECT ORIENTED MODELIGN 10 hours

Use case analysis, Analysis level UML diagrams, Analysis best practices, Role of aggregation,
composition, association, inheritance, delegation, interaces, Examples and case studies.

4. OBJECT ORIENTED DESIGN 10 hours

Design best practices, Design patterns, Creational patterns, Structural patterns, Behavioural
patterns, Role of patterns in object oriented design, Examples and case studies

5. DISTRIBUTED OBJECTS AND COMPONENT TECHNOLOGY 10 hours

Distributed object computing, Concept of object request broker, Interface definition language
(IDL). Common object request broker architecture (CORBA). Component technology, Reusing
components, Bioinformatics components, Object oriented frameworks.

6. OBJECT ORIENTED DATABASES 10 hours

Limitations of flat files, Advantages and disadvantages of relational databases, Need for object
oriented databases, Object relational databases, Mapping from objects to relational or object
relational databases, Examples and case studies in bioinformatics.

RECOMMENDED BOOKS

MAIN READING

1. J. Rumbaugh, M. Blaha, W. Premerlani, F. Eddy, and W. Lorenson, Object-oriented Modelling

and Design, PHI, EEE, 1997 (Available in Indian Edition)
2. G. Booch, J. Rumbaugh, and I. Jacobson, I. The Unified Modeling Language User guide.
Addison-Wesley 1999 (Available in Indian Edition)

SUPPLEMENTARY READING

1. E.Gamma, R Helm, R. Johnson, and J. Vlissides, Design Patterns : Elements of Reusable Object
Oriented Software. Addison-Wesley, 1995 (Available in Indian Edition)

2. G. Booch, Object Oriented Analysis and Design with Applications, Second Edition, Benjamin
Cummings, 1994 (Available in Indian Edition)

3. Jim Conallen, Building Web Applications with UML. Addison-Wesley, 2000 (available in Indian
Edition)

58
 BI-B5.3-R0 : COMPUTATIONAL PROTEOMICS AND GENE EXPRESSION STUDIES

Objective of the Course

On completion of this course, students will have been exposed to computational problems which arise in
the analysis for data from high throughput proteomic and genomic platforms.

.
Outline of Course

S. No. Topic Minimum No. of Hours

1. Introduction to Gel Electrophoresis 6
2. Introduction to Mass Spectrometry 6
3. Introduction to Microarrays 6
Sequencing Hybridization and Mass
4. 7
Spectrometry
5. Image Analysis Basis 15
6. Statistics for Hypothesis Testing 6
7. Clustering Algorithms 8
8. Class Prediction Algorithms 6
Lectures = 60
Practicals / Tutorials = 60
Total = 120

Detailed Syllabus

1. Introduction to Gel Electrophoresis 6 hours

Physical Principles behind Electrophoresis

Application to Genomics and Proteomics
Overview of Computational Problems in Electrophoresis:
Lane Detection, Spot recognition, Image Matching

2. Introduction to Mass Spectrometry 6 hours

Physical Principles of Spectrometry

Applications to Genomics and Spectrometry
Overview of Computational Problems in spectrometry:
Peptide Sequencing, Peak Picking

3. Introduction to Microarrays 6 hours

Physical Principles of Microarrays

Applications to Genomics and Sequencing
Overview of Computational Problems in Microarrays:
Gridding, Spot Recognition and Segmentation, Hypothesis Testing
Clustering, Class Prediction

4. Sequencing by Hybridization and Mass Spectrometry 7 hours

Sequencing Algorithms

59
5. Image Analysis Basics 15 hours

Working with Image Formats: TIFF, PGM, JPEG

Edge Detection
Segmentation
Line Detection
Image Alignment
Microarray Gridding

6. Statistical Hypothesis Testing 6 hours

Normal Distribution
T and F Distributions
T-Test and ANOVA
Permutation Testing

7. Clustering Algorithms 8 hours

Distance Metrics
K-Means, Hierarchical Clustering
Visualizing Clustering Results
Application of Clustering

8. Class prediction Algorithms 6 hours

Decision Trees and Bayesian Methods

Introduction to Neural Networks

RECOMMENDED BOOKS

MAIN READING

1. Microarray Gene Expression Data Analysis: A Beginner’s Guide, Helen. C Caustn Blackwell
Publishers, 2003

2. Microarray Analysis, Mark Schena, Wiley-Liss, 2002

3. DNA Microarraya and Gene Expression: From Experiments to Data Analysis and Modeling.
Pierre Baldi (Author), G. Wesley Hatfield (Author) and Wesley G. Hatfield, Cambridge University
Press, 2002

4. Microarray Bioinformatics, Dov Stekel, Cambridge University Press, 2003

SUPPLEMENTARY READING

1. Microarrays for an integrative Genomics, Issac S. Kohare, Alvin T. Kho and Atul J. Butte, MIT
Press reprinted by Ane Books, New Delhi 2004

2. DNA Array Image Analysis by Gerda Kamberova, Shishir Shah.

60
 BI-B5.4.1-R0: COMPUTER AIDED MOLECULAR MODELLING AND DRUG DISCOVERY

Objective of the Course

The course is designed keeping in view an undergraduate student with plus two level knowledge in
Physics, Chemistry and Mathematics, and elementary knowledge in Biology. The student also needs to
have some exposure to use of computers. The objective of the course is to familiarize the student with
basic concepts in analog and target structure based (rational) drug designing. The focus is on
comparisons of structural and electronic parameters amongst different molecules and scoring methods to
rank the ligand making use of “Principle of similarity” with other known ligand or “complimentary” with the
active site of the target molecule. To achieve this, the student would be familiarized with building small
molecules, computation of structure based and electronic parameters, docking a small molecule in the
active cavity and setting up of QSAR (quantitative structure activity relationship) method.

Learning outcome

At the end of the course, the student will be equipped with different skills involved in computer aided drug
designing. He would be able to do molecular modelling, quantum chemical calculations, compute
electronic indices, identify active sites of target molecules and dock a ligand to the target molecule. He
would also be able to optimise a ligand using different scoring methods.

Outline of Course

S. No. Topic Minimum No. of Hours

1. Introduction to Drug Designing 5
2. Small molecular structures 10
3. Introduction to quantum chemical calculations 15
4. Geometry optimization 10
Basic concepts in quantitative structure activity
5. 5
relationship (OSAR)
Basic principles of target structure based
6. 15
(rational) drug designing
Lectures = 60
Practicals / Tutorials = 60
Total = 120

Detailed Syllabus

1. Introduction to drug designing 5 hours

a. Different approaches to drug designing

b. Basic principle of similarity and complimentarity
c. High throughput vs rational drug designing
d. Use of computer modelling technique to drug designing

2. Small molecular structures 10 hours

a. Different coordinate systems and transformations amongst them

b. Basic Principle 2D and 3D Graphics and use of molecular graphics packages (e.g.
RasMol, RasTop, Qmol, MolMol)

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 c. Cambridge Structural Data base
d. Building small molecules using chemical information
e. Use of Builders and Sketchers (eq. ISIS Draw, HyperChem)

3. Introduction to quantum chemical calculations 15 hours

a. Scrodinger equation, Variation method

b. Roothan’s equation, Uniform & non uniform methods
c. Introduction to molecular orbital methods as : CNDO, INDO, MINDO, PCILO and ab
initio.
d. Computation of HOMO (Highest occupied molecular orbital), LEMO (Lowest empty
molecular orbital), Bond orders, Energies & Electronic indices using packages
e. Computation of Molecular Electrostatic Potential (MEP) maps using packages
4. Geometry optimization 10 hours

a. Use of classical (Empirical potential energy / function and grid search) methods
b. Use of Quantum mechanical approach
c. Use of molecular mechanics methods
5. Basic concepts in quantitative structure activity relationship (QSAR) 5 hours

a. Objective of QSAR
b. Development of Hansch QSAR equation
c. QSAR Descriptors
d. Regression analysis
6. Basic principles of target structure based (rational) drug designing 15 hours

a. Target identification and validation

b. Active site analysis
c. Basic principle of Docking a ligand in active site of a target
d. Builders & Growers
e. Different methods of scoring and Lead optimization

Methodology

The course would be taught through lectures, demonstration and tutorials

RECOMMENDED BOOKS

MAIN READING

1. Molecular Modeling: Basic principles and applications. Holtje HD, sippl W, Rognan D and Folkers
nd
G. Wiley-VFH 2 Edition (2003)
2. Quantum Biology: S. P. Gupta, New Age publishers
3. Molecular modelling and drug design. Andrew Vinter and Mark Gardner and Boca Raton, CRC
Press, 1994
4. Molecular Similarity in drug design, Dean PM, Chapman and Hall, 1995

SUPPLEMENTARY READING

1. Computer assisted Lead finding and optimization: current tools for medicinal chemistry. Han Van
De Waterbeemd (Ed.) Wiley-VCH, 1997
2. Chemical Applications of Molecular Modelling, Goodman, JM Royal Society of Chemistry , 1998
3. Molecular Modelling: Principles and Applications by Andrew R. Leach, Longman, 1996

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4. Computer Aided drug design: Methods and applications: Ed by Thomas J. Perun and CL Propst.
Marcel Dekker, 1989
5. 3D QSAR in Drug Design Theory Methods and Applications – Hugo Kubinyi. Kluwer, 1993
6. Advances in Drug Discovery Techniques Alan L. Harvey (Ed.) John Wiley & Sons, 1998

BI-B5.4.2-R0: CHEMOINFORMATICS

Objective of the Course

The course aims to introduce the fundamentals of Chemoinformatics which are required in computer
aided design. The students will also be exposed to issues related to chemical data processing

Outline of Course

S. No. Topic Minimum No. of Hours

1. Basics of Chemoinformatics 4
Chemoinformatics and computational Tools and
2. 25
Techniques
3. Molecular similarity measures 6
4. High throughput screening 10
5. Quantitative structure-activity relationship 15
Lectures = 60
Practicals / Tutorials = 60
Total = 120

Detailed Syllabus

1. Basics of Chemoinformatics 4 hours

Introduction and Scope of Chemoinformatics – Chemical Information Sources- Structural

representations and file formats – Chemical data formats and standard databases – Area of
application of Chemoinformatics – Property prediction, QSAR, QSPR etc.

2. Chemoinformatics and computational Tools and Techniques 25 hours

Introduction to Chemoinformatics related algorithms – Graph theoretical applications in chemistry

– Chemical information retrieval – 2D searches (structural and substructure searches, similarity
searches), 3D searches (virtual screening, conformational searches, flexible searches), building
queries (pharmacophore generation and validation), Diversity searches and diversity analysis,
Algorithms for diversity analysis – Calculation of structure descriptors – Estimation of Physical
and Chemical properties – Methods of data analysis - Machine learning techniques –
Chemometrics, Statistical techniques – Design of chemical (combinatorial) libraries – Examples
of chemoinformatics software.

Web based chemoinformatics : Molecular data generated in modern drug discovery efforts – Data
– structured numerical annotation /text – graphical overview of the architecture, database access,
similarity and subtractive searches, Library design and reactant solution and filtering

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3. Molecular similarity measures 6 hours

Relavance chemical reasoning and analysis: Molecular representations and their similarity
measures, chemical graphs, discrete and continuous- valued feature vectors, Field based
functions – representations of Molecular fields, chemistry spaces.

4. High throughput screening 10 hours

Practical aspects, clustering and similarity, recursive partitioning, rule based evaluation,
pharmacophore modelling, data sharing issues associated with NCI dataset

Information compound sets – High throughput screening, Methods, techniques and strategies
implemented at Pharmacia, computational methods, custom prioritization software, score
components – q score, molecular complexity estimated stability, scoring strategy Biological score,
important features of scores and statistics

5. Quantitative structure – activity relationship 15 hours

Design of compounds for medicinal use, predicted bioactivity, QSAR virtual throughput
sequencing (VHTS), bioactive data Chiral centres Force fields and partial changes, molecular
confirmations systematic conformation feature – Molecular alignment.

Alignment – free 3D description software and hardware – Description calculation, Molecular

surface, Molecular Lipophilicity, potential calculations

RECOMMENDED BOOKS

MAIN READING

1. Chemoinformatics (Methods in Molecular Biology Vol. 275 Ed. By Jurgen bajorath. Humana
Press 2004
2. Structural Bioinformatics. Ed. By P. E. Bourne and H. Weissig. Wiley-Liss 2003
3. J. Gasteiger “Chemoinformatics: A text book” John Wiley and Sons 2003

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SEMESTER – VI

Project

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