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CURRICULUM FOR M.Sc.

IN BIOINFORMATICS
SESSION 2005-2007
Brijesh Singh Yadav(brijeshbioinfo@gmail.com)

Paper Code Nomenclature of paper Max/(Min) Marks Total


(Th./Prac.) Int. / Sess.
M.Sc. (Bioinformatics) First Semester
MBI-101 (B)* Basic Mathematics 80(29) 20(10) 100
MBI-102 (T) Introduction to Bioinformatics 80(29) 20(10) 100
MBI-103 (T) Introduction to Concept in Computing & Computer 80(29) 20(10) 100
Programming
MBI-104 (T) Internet Technology & Distributed Computing 80(29) 20(10) 100
MBI-105 (T) Cell Biology & Genetics 80(29) 20(10) 100
MBI-106 (P) S/W Lab I – Problems based on MBI-103 80(40) 20(10) 100
MBI-107 (P) S/W Lab II – Problems based on MBI-104 80(40) 20(10) 100
M.Sc. (Bioinformatics) Second Semester
MBI-201 (T) Biological Database, Data Mining & Data Security 80(29) 20(10) 100
Techniques
MBI-202 (T) Introduction to Database System 80(29) 20(10) 100
MBI-203 (T) Programming in Object Oriented Languages 80(29) 20(10) 100
MBI-204 (T) Pharmacology & Chemoinformatics 80(29) 20(10) 100
MBI-205 (T) Structural Biology 80(29) 20(10) 100
MBI-206 (P) S/W Lab III – Problems based on MBI-202 80(40) 20(10) 100
MBI-207 (P) S/W Lab IV – Problems based on MBI-203 80(40) 20(10) 100
MBI-208 (MP) Minor Project 80(40) 20(10) 100
M.Sc. (Bioinformatics) Third Semester
MBI-301 (T) Computer Graphics & Visualization 80(29) 20(10) 100
MBI-302 (T) Machine Learning Techniques (Advanced Computing) 80(29) 20(10) 100
MBI-303 (T) Genome to Drug & Vaccine 80(29) 20(10) 100
MBI-304 (T) Metabolomes & Metabolic Pathway 80(29) 20(10) 100
MBI-305 (T) Emerging Areas in Bioinformatics 80(29) 20(10) 100
MBI-306 (P) S/W Lab V – Problems based on MBI-301 80(40) 20(10) 100
MBI-307 (P) S/W Lab VI – Problems based on MBI-302 80(40) 20(10) 100
M.Sc. (Bioinformatics) Fourth Semester
MBI-401 (T+P) Seminars on Applications of Bioinformatics in 100(50) 100(50) 200
Agriculture/ Human Health/ Environment/ Biotechnology/
Molecular Biology/ Neurobiology/ Drug Designing/
Veterinary Sciences
MBI-402 (PP) Research Paper Presentation 100(50) 100(50) 200
MBI-403 (PR) Major Project 200(100) 200(100) 400
Grand Total of Marks = 3000

* Students from mathematics/ Computer Stream will study paper MBI-101(A)* of Basic Biology,
whereas students from biology/ agriculture stream will study paper MBI-101(B)* of Basic
Mathematics.
Department of Computer Science, A.P.S. University, Rewa (M.P.)
Syllabus for M.Sc. Bioinformatics - First Semester
(Session 2004-2006)
PAPER (MBI-101(B)) BASIC MATHEMATICS.
Max.Marks. 80
Time: 3 hours Min.Marks. 29

Unit I
• Calculus: Limits, Complete Differentials, Partial differentials of functions with
one variable and multiple variables.
• Integration: Elementary Integration, Definite and Non-definite integral; Series,
Logarithms.
• Differential Equation: Ordinary differential equations (first order), Partial
differential equations.

Unit II
• Vector : Addition, subtraction, dot, cross, scalar triple product, divergence, curl of
a vector, equation of normal
• Matrix algebra: Addition, subtraction, multiplication, transpose inverse, and
conjugate of matrix etc.
• Trigonometric functions: Sin, Cos, Tan, Cot, Series expansion of these functions
and other related functions

Unit III
• Correlation, Covariance, Calculation of covariance
• Correlation analysis, Types of correlation, Scatter Diagram
• Regression analysis, Regression coefficients
• Probability Terms and concepts
• Definition, Simple problems involving probability

Unit IV
• Introduction to Biostatistics
• Measures of central tendency, Mean, Median, Mode, Mean Deviation, Standard
Deviation
• Chi-Square Test, Degrees Of Freedom, Chi-Square Distribution, Properties of
Chi-Distribution

References:
• P.N. Arora,P.K. Malhan ,Biostatistics ,Himalaya Pub.
• Mohan.P. Arora,Fundamentals Of Genetics,Himalaya Pub
• P.N.Arora : Fundamentals Of trigonometry and Matrix
• Manjeet Singh: Simple approach to calculus

Note: In all there will be NINE questions. Two questions are to be asked from each of the four units (with internal choice in
each unit). The students are expected to attempt only one question from each unit. The ninth question will consist of four
short notes (one from each unit), out of which only two are to be attempted.
Department of Computer Science, A.P.S. University, Rewa (M.P.)
Syllabus for M.Sc. Bioinformatics - First Semester
(Session 2004-2006)
PAPER (MBI - 102 (T) INTRODUCTION TO BIOINFORMATICS
Max.Marks. 80
Time: 3 hours Min.Marks. 29

Unit I
• INTRODUCTION
• Overview of bioinformatics
• Resources
• Genome projects
• Pattern recognition and prediction

Unit II
• DATABASES AND DATA RETRIEVAL
• DNA Sequence Databases (GenBank, EMBL)
• Protein Sequence Databases (SWISS-PROT, PROSITE)
• Data/Sequence Retrieval From Databases
• Genome Databases - Searching And Data Retrieval
Unit III
• SIMILARITY/HOMOLOGY SEARCHING
• Sequence Comparison/Homology searchers
• BLAST
• How BLAST Works
• PSI-BLAST
• BLASTing Against Specific Genomes
• FASTA
• Working of FASTA

Unit IV
• SEQUENCE ANALYSIS
• Sequence Alignment
• Global and Local Alignment
• Pair wise and Multiple sequence alignment
• PAM and BLOSUM
• CLUSTALW
• Molecular phylogeny
• Making tree
• DNA/PROTEIN SEQUENCE ANALYSIS AND MANIPULATION
• Open Reading Frame (ORF) Identification
• Promoter Prediction And Analysis
• DNA Restriction Analysis
• DNA Sequence Translation To Amino Acid Sequence
• Codon Usage analysis
• General Programs Of Interest
Reference:
• Attwood, T.K. and Parry-Smith, D. J. Introduction to Bioinformatics, Longmans
• S. Sundara Rajan, R. Balaji, Introduction to Bioinformatics, Himalaya Pub.
Note: In all there will be NINE questions. Two questions are to be asked from each of the four units (with
internal choice in each unit). The students are expected to attempt only one question from each unit. The
ninth question will consist of four short notes (one from each unit), out of which only two are to be
attempted.
Department of Computer Science, A.P.S. University, Rewa (M.P.)
Syllabus for M.Sc. Bioinformatics - First Semester
(Session 2004-2006)
PAPER (MBI-103) INTRODUCTION TO CONCEPT IN COMPUTING & COMPUTER PROGRAMMING

Time: 3 hours Max.Marks. 80


Min.Marks. 29

Unit I
• Introduction to computers: Characteristics & capabilities; classification;
Components of computer system with Block Diagram, CPU, only preliminary concept of
Software, Hardware, Low Level Language, High Level Language, Compiler and
Interpreter.
• Introduction to operating Systems: WINDOWS, NT, UNIX/Linux operating
systems.

Unit II
• C Programming Part I: Basics of C programming, Structure of a simple C
program, Simple I/o functions, Data types in C, operators & their precedence, Control
Structures: if-else statements, switch statement, loops: while, do-while and for
loop.Functions: User-defined functions, returning a value from a function, local &
Global variables, automatic, Static Register and External Storage class. Parameters:
Type, declaration of a function, functions with more than one parameters, recursion,
Arrays: arryas (upto 2 dimensions), Declaration and initialization, the break structured,
string and character arrays, operations with arrays, The C preprocessors.

Unit III
• C Programming part II: String and string functions: Pointers, the concept of
pointers, the address and indirection operators, passing pointers as parameters. Dynamic
memory allocation, Arrays and pointers, Passing by value and reference, Address
arithmetic. Pointer to pointers, Structures: Initializing a structure, Arrays of strucgtures,
arrays within structures, structures within structures; Structures and functions, Unions,
Files in C, modes for files, functions used in files (putchar, getchar, getc, putc, fopen,
fclose, fscanf, fprint,fseek, ftell, fread and (write), error handling in files.

Unit IV
• Data structure : Introduction: Algorithm analysis for time and space
requirements, introduction to stack, queue, linked list, doubly linked lsit, circular linked
list and their applications; Polynomial manipulation, multiple precision, fixed block
storage allocation, dynamic storage management, first fit and best fit storage allocation,
garbage collection, compaction. Sorting and searching techniques. (Use of biological
database for case study).

REFERENCE:
• Introduction to comp. : P.K. Sinha
• Gottfried: Programming with C
• E. Balagurusamy: Programming with C
• Horowitz & Sahni: Fundamentals of Data Structures, Comp. Sc. Press
• Tanenbaum A.S.: Data Structures using C, PHI

Note: In all there will be NINE questions. Two questions are to be asked from each of the four units (with
internal choice in each unit).. The students are expected to attempt only one question from each unit. The
ninth question will normally have four parts (one from each unit), out of which only two are to be attempted.
Department of Computer Science, A.P.S. University, Rewa (M.P.)
Syllabus for M.Sc. Bioinformatics - First Semester
(Session 2004-2006)
PAPER (MBI-104) INTERNET TECHNOLOGY & DISTRIBUTED COMPUTING
Max.Marks. 80
Time: 3 hours Min.Marks. 29

Unit I
• Internet: History and evolution of Internet. Internet and intranet, Basic concept
of www, HTTP, FTP, URL, domain name, IP address, web browser, web server,
web page, web site, portals, email, chatting, usenet, telnet, newsgroup, fax,
telephony, telecommuting, conferencing, searching, downloading, uploading,
files on internet, search engines. Email (reading, ending, deleting, replying),
voice and video conferencing. Internet protocol: TCP/IP, dialup access, direct
access, three levels of internet connectivity, ISPs, Introduction to DNS.

Unit II
• Internet Security & HTML: Overview of internet security, access security,
transaction security, security zones, digital IDS, sending / receiving signed and
encrypted emails. Introduction to firewalls. Web page design: static and dynamic
web pages. Introduction to HTML, HTML elements and tags, formatting with
HTML tags, physical, logical HTML styles, setting fonts, colors and headings,
displaying plain, presenting and arranging text using <DIV>, <SPAN>,
<LAYERS> tags.

Unit III
• Advance HTML: Working with images, links and lists, creating tables, working
with frames, creating horizontal, vertical frames, named frames, opening new
browser window, creating HTML forms, adding controls on forms, submitting
data from forms, working with multimedia, multimedia sound, video, 3D using
multimedia files, inline sound and videos. Style sheets: types, creating and using
style sheets.

Unit IV
• Java Script and XML: Introduction to client and server side scripting.
Introduction to Java script, data types, operators, conditional statement, loops in
Java script, functions, arrays, objects and elements in Java script, Form validation
using Java script. Introduction to XML, creating XML, documents, specifying
attributes in DTDs, accessing XML data with XML Data Island, documents.
Handling events while loading XML documents.

References:
• The Internet: Christian Crumlish
• HTML Complete: BPB Publication
• Internet Complete: BPB Publication
• Teach yourself Internet in 24 hours: Techmedia.
Note: In all there will be NINE questions. Two questions are to be asked from each of the four units (with internal choice in
each unit). The students are expected to attempt only one question from each unit. The ninth question will consist of four
short notes (one from each unit), out of which only two are to be attempted.
Department of Computer Science, A.P.S. University, Rewa (M.P.)
Syllabus for M.Sc. Bioinformatics - First Semester
(Session 2004-2006)
PAPER (MBI-105) CELL BIOLOGY & GENETICS
Max.Marks. 80
Time: 3 hours Min.Marks. 29

Unit I

Cell Biology
• Prokaryotic and eukaryotic cells; membranes and cellular compartmentation; An
overview of organelles, (mitochondria, chloroplasts, ER, Golgi, lysosomes and
peroxisomes; nucleus and nucleolus) and organelle genetic systems.
• Cellular membranes : Structure, transport, channels, carriers, receptors,
endocytois, membrane potentials.
• Cell motility and shape : cytoskeletal elements, cilia and flagella; motor proteins.
Unit II
• Cell-cell interactions and signal transduction: Intercellular junctions, signaling
by hormones and neurotransmitters; receptors, G-proteins, protein kinases and
second messengers.
• Protein traffic in cells : Protein sorting and signal sequences; protein
translocation in ER and vesicular transport to Golgi, lysosmes and plasma
membrane; protein import into nuclei, mitochondria, chloroplasts and peroxisomes.
• Cell cycle and its regulation; events during mitosis and meiosis
Unit III
• Genetics
• Science of genetics – objectives, terminologies, methods.
• Mendelian principles of inheritance, sex linked inheritance.
• Concept of linkage, linkage maps and recombination.
• Mutations – molecular, gene/point and chromosomal.
Unit IV
• Phenotype and genotype relationships, role of environment, from gene to
phenotype, gene interactions
• Study of quantitative traits.
• Genetics of populations, genetics and evolution.
• Genetics and diseases, cancer.

References
1. The world of the cell, 4th edition. Becker, Kleinsmith & Hardin.
2. Cell, A Molecular Approach,2nd edition, GM Cooper
3. Fundamentals of Genetics, Mohan P Arora

Note: In all there will be NINE questions. Two questions are to be asked from each of the four units (with internal choice in
each unit). The students are expected to attempt only one question from each unit. The ninth question will consist of four
short notes (one from each unit), out of which only two are to be attempted.
Department of Computer Science, A.P.S. University, Rewa (M.P.)
Syllabus for M.Sc. Bioinformatics - First Semester
(Session 2004-2006)
PAPER (MBI-106) : S/W LAB I – PROBLEMS BASED ON MBI-103
Max.Marks. 80
Min.Marks.40
Part-A
1. Write a C program to create a doubly linked list and arrange the list in ascending sorted
order of information. Information field is of type integer.
2. Write INSERT and DELETE functions in C language, simulating insertion and deletion
operations of a queue, which is implemented by singly linked list. Make necessary
assumptions.
3. Write a general, non-recursive C program for postorder traversal of a binary tree.
4. Write a C program for selection and bubble sort.
5. Write a C program to evaluate the postfix expression P using stack. Explain the
execution of the program with the example
P: 562 + * 124/- (5 # 6 # 2 # + # * # 12 # / # -) (# stands for a blank space)
6. Write PUSH and POP functions in C language, simulating push and pop operations of a
stack, which is implemented by a singly linked list. Make necessary assumption.
7. Write a C program to print the information, from each node in reverse order in a doubly
linked list, in which pointer to last node is TAIL.
8. Write a C program that
a) counts the number of nodes in a liked list
b) will concatenate two linked lists. The function should have two parameters, pointers
to the beginning of the list, and the function should link the end of first list to the
beginning of the second.
9. Write a program that will split a linked list into two linked lists, so that successive nodes
go to different lists (the 1st, 3rd and all odd numbered nodes go to the first list and the
2nd,4th and all even numbered nodes go to the second).
10. Write a C program to carry out Binary Search on a tree.

Part-B
1. Write a C function to insert an item into a hash table with open addressing and linear
probing.
2. Write a C program to find the shortest path in a given weighted graph.
3. Write a program to correct rudimentary syntax errors like unbalanced parenthesis, brackets
and braces. Don’t forget about single and double quotes, escape sequences and
comments.
4. Write a program to implement a circular queue as a linked list.
5. Design the algorithm and generate a program to perform an in-fix to post-fix conversion.
6. Design a function to obtain the mirror image of binary tree and demonstrate its functioning
with a C program.
7. Write a program, which will convert a singly linked list into a binary tree.
8. Write a program, which will convert binary tree into a binary search tree.
9. Write a program to search a given numbers in a linked list and print the output a found or not
and no. of occurrences (if so).
10. Write a program for indenting of a C program.
Department of Computer Science, A.P.S. University, Rewa (M.P.)
Syllabus for M.Sc. Bioinformatics - Second Semester
(Session 2004-2006)
MBI - 201 (T) BIOLOGICAL DATABANKS, DATA SECURITY AND DATA MINING TECHNIQUES

Max.Marks. 80
Time: 3 hours Min.Marks. 29

Unit I
• Data warehousing, data capture, data analysis
• Introduction to Nucleic Acid and Protein Sequence Data Banks
• Nucleic acid sequence data banks: Genbank, EMBL nucleotide sequence data
bank, AIDS Virus sequence data bank, rRNA data bank
• Protein sequence data banks: NBRF-PIR, SWISSPROT, Signal peptide data bank

Unit II
• Database Similarity Searches: BLAST, FASTA, PSI-BLAST algorithms
• Pair wise sequence alignment - NEEDLEMAN and Wunsch, Smith Waterman
algorithms
• Multiple sequence alignments - CLUSTAL, PRAS

Unit III
• Patterns, motifs and Profiles in sequences:
 Derivation and searching,
 Derived Databases of patterns, motifs and profiles: Prosite, Blocks,
Prints-S, Pfam, etc.
 Primer Design

Unit IV
• Data Security
 Science and study of methods of protecting data: Discretionary and
mandatory access controls, secure database design, data integrity, secure
architectures, secure transaction processing, information flow controls,
inference controls, and auditing. Security models for relational and object-
oriented databases. Security of databases in a distributed environment.
Statistical database security.

References :
• Baxevanis, A.D. & Ouellettee, B.F.F.: Bioinformatics: a practical guide to the analysis of
genes and proteins. (2nd. Ed.) New York. Wiley Interscience, 2001.
• Mount, D. W.: Bioinformatics: Sequence and Genome Analysis. Cold Spring Harbor.
CSHL Press, 2001.
• Marshall D. Abrams, Sushil Jajodia, and Harold J. Podell, eds. Information Security: An
Integrated Collection of Essays, IEEE Computer Society Press, 1995.

Note: In all there will be NINE questions. Two questions are to be asked from each of the four units (with internal choice in
each unit). The students are expected to attempt only one question from each unit. The ninth question will consist of four
short notes (one from each unit), out of which only two are to be attempted.
Department of Computer Science, A.P.S. University, Rewa (M.P.)
Syllabus for M.Sc. Bioinformatics - Second Semester
(Session 2004-2006)
MBI - 202 (T) INTRODUCTION TO DATABASE SYSTEMS
Max.Marks. 80
Time: 3 hours Min.Marks. 29

UNIT I
 Basic Concept: An Introduction to database System, Basic Data System
Terminology, Purpose of DBMS, Data Independence, An Architecture of
DBMS: Schema, Subschema, mapping, Physical & Logical Data, Basic File
Systems, File Organization: Sequential, Index Sequential, Hosting, B-Tree
based index, File Organisation based on Dynamic Hashing with immediate
splitting, Model of Real World, Details of E-R Model.

UNIT II
 Three Data Models: An Overview of three Main Data Models i.e.
Hierarchical Model, Network Model, Relational Model and their Inter
comparison, Concept of Relation, Relational Algebra: Basic Operation like
Union, Intersection, Difference, Product Join, The relational Calculus:
Domain & Tuple Calculus, Relational Database Design: Integrity Constraints,
Functional Dependency: Single Value and Multi Value Functional
dependency, Normal Forms: I, II, III, Boycee Codd, & IVth Normal forms;
Join Dependency.

UNIT III
 Query Processing & Database Software: Query Interpretation,
Equivalence of Expression, Estimation of Query Processing Cost, Query
Optimization by Algebraic Manipulation, Join Algorithms, Types of Data
Base Languages: Procedural and Non-procedural Language, Relational
Commercial Query languages,QBE, SQL: Introduction, Basic Structure, the
Power of SQL (Creation, Insertion, Deletion, Indexing & Modification of
Databases in SQL), query optimization strategies.

UNIT IV
 Management Considerations & Future Trends: Security & Integrity:
Introduction, Access Control, Crypto Systems, Statistical DataBase Security;
Concurrency Control: Transaction, Database System Architecture,
Serializability, Locking, Database Recovery: Kinds of Failure, Recovery
Techniques, Object, An Overview of Oriented Model, Distributed database:
Structure, Tradeoffs, Design, Client Server Database, Knowledge databases.

Text Books:
1. Henry F. Korth & A. Silbershatz: Data Base System Concepts, MGH
2. Arun K. Majumdar & P. Bhattacharya: Data Base Management System, TMH

Reference Books
1. Jeffrey O. Ullman : Principles of Database Systems, Galgotia Pub. Co. Ltd.
2. Bipin C. Desai: An Introduction to Database Systems, Galgotia Pub. Co. Ltd.
3. James Martin: Principles of Database Management, PHI
4. James Martin, Computer Database organization, PHI

Note: In all there will be NINE questions. Two questions are to be asked from each of the four units (with internal choice in
each unit). The students are expected to attempt only one question from each unit. The ninth question will consist of four
short notes (one from each unit), out of which only two are to be attempted.
Department of Computer Science, A.P.S. University, Rewa (M.P.)
Syllabus for M.Sc. Bioinformatics - Second Semester
(Session 2004-2006)
MBI - 203 (T) PROGRAMMING IN OBJECT ORIENTED LANGUAGES
Max.Marks. 80
Time: 3 hours Min.Marks. 29

Unit I
JAVA
• An introduction to JAVA programming
• Object oriented programming and Java
• Java Basics, Working with objects, Arrays, Conditionals and Loops
• Creating Classes and Applications in Java, More about methods
• Java Applets Basics, Graphics, Fonts and Color.
• Simple Animation and Threads, Advanced Animation, Images and Sound
• Managing Simple Events and Interactivity
• Creating User Interfaces with AWT

Unit II
• Windows, Networking and other Tidbits, Modifiers, Access Control and Class
Design.
• Packages and Interfaces, Exception, Multithreading, Streams and I/O.
• Using Native Methods and Libraries, Under the Hood, Java Programming Tools.
• Working with Data Structures and Java
• Image Filters

Unit III
Programming Visual Basic
• Introduction to Application Development using Visual Basic
• Working with Code and Forms
• Variables, Procedures and Controlling Program Executor
• Standard Controls

Unit IV
• Data Access Using Data Control
• Connecting to Oracle Database using Visual Basic

References:
• Java by dissestion , Ira Pohl and Charlie Mc Dowell, Addison Wesley.
• Java Software Solutions , John Lewis and William Loftus, Addison Wesley
Java for Computer Information Systems , Andrew Stangaard , Prentice Hall.
• Data Structures and Algorithms in Java (Edition ), Michael T. Goodrich, Roberto
Tamassia, John Wiley.
• VB6 Unleashed – Techmedia.
• Using Visual Basic 6, Que.

Note: In all there will be NINE questions. Two questions are to be asked from each of the four units (with internal choice in
each unit). The students are expected to attempt only one question from each unit. The ninth question will consist of four
short notes (one from each unit), out of which only two are to be attempted.
Department of Computer Science, A.P.S. University, Rewa (M.P.)
Syllabus for M.Sc. Bioinformatics - Second Semester
(Session 2004-2006)
MBI 204 (T) BIODIVERSITY INFORMATICS AND CHEMOINFORMATICS
Max.Marks. 80
Time: 3 hours Min.Marks. 29

Unit I
• Introduction: Biological information, biological diversity of life, species
diversity: taxonomic information on plants, animals, microbes and viruses.
Genetic diversity, Ecological/ Ecosystem diversity, Urban biodiversity,
methods for species identification and classification, biodiversity databases and
software for identification.

Unit II
• Immunology : Overview of immune system, innate and acquired immune
system, Characteristics of B Cell and T Cell antigens, Autoimmunity, Ligand-
receptor interaction in the light of protein structure in immune system, Use of
bioinformatics in immunology and vaccine development

Unit III
• Chemoinformatics: History, current activities and challenges in the
chemoinformatics, Chemical information and sources, Major chemical databases and
information retrieval, Chemical Structure drawing tools.

Unit IV
• Pharmacology and drug discovery, Pharmacodynamics and pharmacokinetics, Drug
potency and Efficacy, Docking, Active site, Pharmacophore identification,
Absorption, Development of a drug: Classical steps, Chemical Parameters in drug
design, Structure based drug discovery, Quantitative Structure Activity
Relationships.

Reference:
PANKHURST, R.J.: Practical taxonomic computing. 1991.

Note: In all there will be NINE questions. Two questions are to be asked from each of the four units (with internal choice in
each unit). The students are expected to attempt only one question from each unit. The ninth question will consist of four
short notes (one from each unit), out of which only two are to be attempted.
Department of Computer Science, A.P.S. University, Rewa (M.P.)
Syllabus for M.Sc. Bioinformatics - Second Semester
(Session 2004-2006)
MBI 205 (T) STRUCTURAL BIOLOGY / MOLECULAR BIOLOGY
Max.Marks. 80
Time: 3 hours Min.Marks. 29
Unit I
• Internal and external co-ordinate system
• Generation of co-ordinates of biopolymers in Cartesian and cylindrical polar co-ordinate
system
• Methods of single crystal X-ray Diffraction of macromolecules: molecular replacement
method and direct method
 Fiber diffraction
 Analysis of structures and correctness of structures
 Submission of data to PDB: atomic coordinates and electron density maps
Unit II
• Anatomy of Proteins
 Ramachandran plot
 Secondary structures
 Motifs
 Domains
 Tertiary and quaternary structures
• Anatomy of DNA: A, B, Z DNA, DNA bending etc.
• RNA structure
• Structure of Ribosome
• Principles of Protein Folding
• Structural data banks - Protein Data Bank, Cambridge small molecular crystal structure
data bank
• Calculation of conformational energy for bio-macromolecules
Unit III
• Methods for Prediction of Secondary and Tertiary structures of Proteins
 Knowledge- based structure prediction
 Fold recognition
 Ab initio methods for structure prediction
• Methods for comparison of 3D structures of proteins
• Methods to predict three dimensional structures of nucleic acids, rRNA
• Electrostatic energy surface generation
Unit IV
• Molecular Mechanics & Molecular Dynamics of Oligopeptides, Proteins, Nucleotides, &
small Molecules
 Mechanics and dynamics of bio-macromolecules
 Simulation of molecular mechanics and dynamics
 Simulations of Free Energy changes
 Force fields
• Molecular interactions of
 Protein – Protein
 Protein – DNA
 Protein – carbohydrate
 DNA – small molecules etc.
• Docking of Molecules
• Molecular Design
References
• Creighton, T. E. Ed.: Protein Structure: A Practical Approach. 1989.
• Creighton, T.E.: Proteins: Structure And Molecular Properties. Second Edition. New York. W. H.
Freeman And Company, 1993.
• Creighton,T.: Protein Folding, 1992.
• Sternberg, M.J.E.: Protein structure prediction: a practical approach, 1996
• Pain, R.G.: Mechanisms of protein folding, 1994
• Leach.A.R: Molecular modelling: principles and applications
Note: In all there will be NINE questions. Two questions are to be asked from each of the four units (with internal choice in
each unit). The students are expected to attempt only one question from each unit. The ninth question will consist of four
short notes (one from each unit), out of which only two are to be attempted.
Department of Computer Science, A.P.S. University, Rewa (M.P.)
Syllabus for M.Sc. Bioinformatics - Third Semester
(Session 2004-2006)
MBI - 301 (T) COMPUTER GRAPHICS AND VISUALIZATION
Max.Marks. 80
Time: 3 hours Min.Marks. 29

UNIT I
Overview of Graphics Systems and 2D Transformation:
Display Devices, Hardcopy devices, Interactive Input Devices, Display processors, Graphics
Software. Output Primitives: Points and lines, Line drawing algorithms, Circle generating
algorithms Basic Transformations, Matrix Representations and Homogeneous Coordinates,
Composite Transformations, Reflection, Shear, Raster methods for transformations. Windowing
and Clipping : Windowing concepts, Clipping algorithms, Window-to-Viewport transformation.

UNIT II
3D Transformation , Viewing and Modeling:
Three Dimensional Transformations : Basic transformations, Rotation about an arbitrary axis,
Reflections, Shears, Transformations of coordinate system. Projections, Viewing
transformations, Software implementation, Hardware implementation. Hidden surface & Hidden
line removal : Classification, Back face removal, Depth Buffer method, Scan line method,
Hidden line elimination, Curved surfaces. Shading and color models : Modeling light intensities,
Displaying light intensities, Surface shading methods, Color models. Modeling methods : Basic
concept, Master coordinates and modeling transformation structured display files, symbol
operations.

UNIT – III
Overview of Multimedia: Introduction, Application of multimedia, terminology, multimedia
enabling technologies in digital representation, Hardware & Software requirement, multimedia
standard, hypertext; History, nature, links, navigation & structure. The nature of sound,
digitizing sound, processing sound, compression format, MIDI, Combining, source & picture,
Video & image processing: Digitizing video, video standards video compression, digital video
editing and post production, streamed video and video conferencing.

UNIT – IV
Animation: Captured animation and image sequences, digital cel and sprite animation, key
frame animation, 3D animation, Combining media: synchronization based presentation: SMIL
(synchronize multimedia integration language), synchronize presentation (HTML + TIME),
accessibility. knowledge base multimedia, future direction. ECMAScript syntax outline,
Multimedia and network: network and transport protocols, multicasting, application protocols for
multimedia: HTTP, caching; Quality of service, server side computation.

Text Books :
1. D. Hearn and Baker : Computer Graphics, Prentice Hall of India Pvt. Ltd.
2. Steven Harrington : Computer Graphics, MGH.
3. Chapman,Wiley; Digital Multimedia,
4. J.D.Foley, A.Van Dam - Fundamentals of Interactive Computer Graphics.
5. David F. Rogers. - Procedural Elements for Computer Graphics
6. David F. Rogers, J.A.Adams - Mathematical Elements for Computer Graphics

Reference Book:
1. Newman and R.F. Sprouli : Principles on Interactive Computer Graphics, MGH.
2. W.K. Giloi : Interactive Computer Graphics, PHI.
3. R.A. Piastock and G. Kalley : Theory and Problems of Computer Graphics, MGH
4 John F. Kloegel Buford; Multimedia System

Note: In all there will be NINE questions. Two questions are to be asked from each of the four units (with internal choice in
each unit). The students are expected to attempt only one question from each unit. The ninth question will consist of four
short notes (one from each unit), out of which only two are to be attempted.
Department of Computer Science, A.P.S. University, Rewa (M.P.)
Syllabus for M.Sc. Bioinformatics - Third Semester
(Session 2004-2006)
MBI - 302 (T) MACHINE LEARNING TECHNIQUES IN BIOINFORMATICS
Max.Marks. 80
Time: 3 hours Min.Marks. 29

Unit I - Introduction
Biological data in digital symbol sequences, genomes – Diversity, size and structure, proteins
and preteomes, on the information content of biological sequences, prediction of molecular
function and structure.
Machine-Learning Foundations: The probabilistic framework, Introduction: Bayesian Modeling,
the cox jaynes axioms, Bayesian inference and induction, model structures: graphical models and
other tricks, summary.
Probabilistic Modeling and Inference: Examples, the simplest sequence models, statistical
mechanics.

Unit II – Machine Learning Algorithms


Introduction, dynamic programming, gradient descent, EM/GEM algorithms, Markov-Chain
Monte-Carlo methods, simulated annealing, evolutionary and genetic algorithms, learning
algorithms: miscellaneous aspects.
Neural Networks: The theory, introduction, universal approximation properties, priors and
likelihoods, learning algorithms: backpropagation.
Neural Networks: Applications, sequence encoding and output interpretation, sequence
correlations and neural networks, prediction of protein secondary structure, prediction of signal
peptides and their cleavage sites, applications for DNA and RNA nucleotide sequences,
prediction performance evaluation, different performance measures.

Unit III
Introduction, Prior information and initialization, likelihood and basic algorithms, learning
algorithms, applications of HMMs: General aspects.
Hidden Markov Models: Applications, Protein applications, DNA and RNA Applications,
Advantages and limitations of HMMs.
Probabilistic Graphical Models in Bioinformatics: The Zoo of graphical models in
bioinformatics, Markov Models and DNA symmetries, Markov Models and Gene finders, Hybrid
models and neural network parameterization of graphical models, the single-model case,
Bidirectional Recurrent neural networks for protein secondary structure prediction.

Unit IV
Probabilistic Models of Evolution: Phylogenetic Trees, Introduction to probabilistic Models of
evolution, substitution probabilities and evolutionary rates, rates of evolution, data
likelihood, optimal trees and learning, parsimony, extensions.
Stochastic grammars and linguistics: Introduction to formal grammars, formal grammars
and the Chomsky hieararchy, applications of grammars to biological sequences, prior
information and initialization, likelihood, learning algorithms, applications of SCFGs,
experiments, future directions.
Microarrays and Gene expression: Introduction to Microarray data, probabilistic
modeling of Array Data, clustering, gene regulation.

Reference:

Note: In all there will be NINE questions. Two questions are to be asked from each of the four units (with internal choice in
each unit). The students are expected to attempt only one question from each unit. The ninth question will consist of four
short notes (one from each unit), out of which only two are to be attempted.
Department of Computer Science, A.P.S. University, Rewa (M.P.)
Syllabus for M.Sc. Bioinformatics - Third Semester
(Session 2004-2006)
MBI - 303 (T) FROM GENOME TO DRUGS
Max.Marks. 80
Time: 3 hours Min.Marks. 29

Unit I
From Genomes to Drugs with Bioinformatics: The molecular basis of disease, the molecular
approach to curing diseases, finding protein targets, genomics vs preteomics, developing drugs, a
bioinformatics landscape, the intrinsic view, the extrinsic view, drug screening, scenario 3:
genetic variability. Database searching : single sequence heuristic algorithms, alignment and
search statistics, multiple sequence alignment, multiple alignment and database searching,
protein families and protein domains, conclusion.
Structure, properties and computer identification of Eukaryotic genes: Structural
characteristics of eukaryotic genes, classification of splice sites in mammalian genomes, methods
for the recognition of function signals, search for nonrandom similarity with consensus
sequences, position-specific sensors, accuracy measures, prediction of donor and acceptor splice
junctions, recognition of promoter regions in human DNA, prediction of poly-A sites, gene
identification approaches, annotation of sequences from genome sequencing projects, functional
analysis and verification of predicted genes, internet sites for gene finding and functional site
prediction.
Unit II
From Genomes to Drugs with Bioinformatics: General features of Regulatory regions in
eukaryotic genomes, general functions of regulatory regions, transcription factor binding sites
(TF-sites), sequence features, structural features, structural elements, organizational principles of
regulatory regions, bioinformatics models for the analysis and detection of regulatory regions,
detection of transcription factor binding sites, detection of structural elements, statistical and
biological significance, methods for detection of regulatory regions, regulatory sequences.
Unit III
Homology modeling in Biology and Medicine: Introduction, the concept of homology
modeling, input data, methods, modeling at different levels of complexity, range of targets,
strengths and limitations, validation, side-chain prediction accuracy, protein health, availability,
backbone conformations, side-chain conformational analysis
Protein structure prediction: Overview, definition of terms, structure comparison and
classification, 3D structure prediction, results, remote homology detection, structural genomics,
sequence to structure to function paradigm, validation of predictions, strengths and limitations,
threading, strengths, limitations, accessibility.
Unit IV
Protein-Ligand Docking in Drug Design: Introduction, A taxonomy of docking problems,
application scenarios in structure-based drug design, methods for protein-ligand docking,
docking of combinatorial libraries, molecular docking in practice, preparing input data, analyzing
docking results, software accessibility
Modeling protein-protein and protein-DNA Docking: Introduction, the need for protein-
protein and protein-DNA docking, overview of the computational approach, structural studies of
protein complexes, methodology of a protein-protein docking strategy, Modeling protein - DNA
complexes, method, results, strategies for protein-protein docking, Fourier correlation methods,
other rigid body docking approaches, flexible protein-protein docking, blind trials of protein-
protein docking, energy landscape for protein docking, conclusions. CADD and modeling using
QSAR.

REFERENCE:
1. Bioinformatics-From Genome to Drugs by R . MANNHOLD,H.KUBINYI,
2. H. TIMMERMANN(Thomas lengauer edition)
Note: In all there will be NINE questions. Two questions are to be asked from each of the four units (with internal choice in
each unit). The students are expected to attempt only one question from each unit. The ninth question will consist of four
short notes (one from each unit), out of which only two are to be attempted.
Department of Computer Science, A.P.S. University, Rewa (M.P.)
Syllabus for M.Sc. Bioinformatics - Third Semester
(Session 2004-2006)
MBI - 304 (T) METABOLOMES AND METABOLIC PATHWAYS
Max.Marks. 80
Time: 3 hours Min.Marks. 29

Unit I
• Carbonydrates and lipids, their importance in cells.
• Proteins: Amino acids and peptides; primary, secondary, tertiary and quaternary
structures; protein – protein interactions; sequence homology, functional and
evolutionary relationships of proteins.

Unit II
• Nucleic acids: Bases, nucleotides, RNA and DNA. Different structural forms of DNA,
denaturation and renaturation of DNA, protein-nucleic acid interactions.
• Enzymes: Units of activity, coenzymes and metal cofactors, temperature and pH effects,
Michaelis-Menten kinetics, inhibitors and activators, active site and mechanism of
enzyme action, isoenzymes, allosteric enzymes, regulation by covalent modification.

Unit III
• Organization of metabolic systems: enzyme chains, multienzyme complexes and
multifunctional enzymes, regulatory enzymes and feedback control of metabolic
pathways, energy charge.
• Carbohydrate metabolism: Glycolysis, gluconeogenesis, glycogenolysis, glycogenesis
and pentose phosphate pathway; hormonal control.

Unit IV
• TCA cycle and oxidative phosphorylation
• β -oxidation and biosynthesis of fatty acids.
• Transamination and deamination of amino acids, ketogenic and glucogenic amino acids,
urea cycle
Purine and pyrimidine biosynthesis

Note: In all there will be NINE questions. Two questions are to be asked from each of the four units (with internal choice in
each unit). The students are expected to attempt only one question from each unit. The ninth question will consist of four
short notes (one from each unit), out of which only two are to be attempted.
Department of Computer Science, A.P.S. University, Rewa (M.P.)
Syllabus for M.Sc. Bioinformatics - Third Semester
(Session 2004-2006)
MBI - 305 (T) EMERGING AREAS IN BIOINFORMATICS

Max.Marks. 80
Time: 3 hours Min.Marks. 29

Unit-I
Questions based on Micro-array technology and system biology

Unit-II
Questions based on Bioinformatics in Drug designating

Unit-III
Questions based on ANN and pattern recognition technique applied for bioinformatics

Unit-IV
Questions based on Nano technology and other tools / technology used in Bioinformatics, and
Challenges associated with it.

References:
Internet and recent research papers including the books already mention in various papers related
to topic mention.

Note: In all there will be NINE questions. Two questions are to be asked from each of the four units (with internal choice in
each unit). The students are expected to attempt only one question from each unit. The ninth question will consist of four
short notes (one from each unit), out of which only two are to be attempted.
Department of Computer Science, A.P.S. University, Rewa (M.P.)
Syllabus for M.Sc. Bioinformatics - First Semester
(Session 2004-2006)
PAPER (MBI-103) INTRODUCTION TO CONCEPT IN COMPUTING & COMPUTER PROGRAMMING
Max.Marks. 80
Time: 3 hours Min.Marks. 29

Unit I
• Fundamentals of Computing
• Introduction to operating Systems: WINDOWS, NT, UNIX/Linux operating
systems
• Comparative Advantages of Security (hacking, cracking) Installation, Portability
and Programming of these operating systems
• Computer Viruses

Unit II
• Elements of Programming in ‘C’ - Pointers, Pointers to the functions, Macros and
Programming in C, Graphs, Data structure - Linked List; stack; Queue, Binary
Trees, Threaded Binary trees; File handling in C; Exception handling in C

Unit III
• Use of INTERNET & WWW
• LAN, WAN, MODEM
• Optical Vs. Electronic Networking
• Security of the network, Fire-walls
• Searches on MEDLINE, CD, bibliographic databases.
Unit IV
• Network Goals
• Applications Network
• Network structure
• Network architecture
• Hierarchical networks
• Ethernet and TCP/IP family of protocols
• Transport protocol design

Reference:
• Andrew S. Tanenbaum: Computer Networks

Note: In all there will be NINE questions. Two questions are to be asked from each of the four units (with internal choice in
each unit). The students are expected to attempt only one question from each unit. The ninth question will consist of four
short notes (one from each unit), out of which only two are to be attempted.