LIST OF SUBJECTS TO BE STUDIED FOR PGDBI

Semester / SUBJECT
Semester I /

PGDBI 1.1 Structural Biology

PGDBI 1.2 Biostatistics

PGDBI 1.3 Data structure and Programming in C

PGDBI 1.4 Introduction to Bioinformatics

PGDBI 1.5 Databases and Biological Databases
Semester II /

PGDBI 2.1 Tools of Bioinformatics

PGDBI 2.2 Object Oriented Programming in C++ and Java

PGDBI 2.3 Web and Networking Technologies

PGDBI 2.4 Project
Elective Paper

PGDBI-E-1 Proteomicsand Drug Designing

PGDBI-E-2 Comparative genomics

1

PGDBI 1.1 Structural Biology

UNIT-1

DNA and RNA: types of base pairing – Watson-Crick and Hoogstein; types of double helices A,B,Z and their geometrical as well as structural features; structural and geometrical parameters of each and their comparison; various types of interactions of DNA with proteins, small molecules. RNA secondary and tertiary structures, t-RNA tertiary structure.

Proteins: Principles of protein structure; anatomy of proteins – Hierarchical organization of protein structure - Primary. Secondary, Supersecondary, Tertiary and quaternary structure; Internal coordinates of proteins; Theory, Derivation and significance of Ramachandran Map, protein energetics; protein folding.

UNIT-2

Carbohydrates:
The various building blocks (monosaccharides), configurations and conformations of the building blocks; formations of polysaccharides and structural diversity due to the different types of linkages

Glyco-conjugates: various types (glycolipids, glycoproteins etc); their structures, interactions with various biomolecules.

UNIT-3

Prediction of protein structure, Secondary structure: Basic principles on which the prediction methods of first, second and third generation are based; algorithms of Chou Fasman, GOR methods; Predicting the secondary structures using these methods and analysis; concepts in measuring the accuracy of predictions (Q3, Segment overlap, Mathew’s correlation coefficient etc.)
UNIT-4

Tertiary Structure: Theoretical basis of the methods for structure prediction (sequence similarity / identity of target protein with proteins of known structure, fundamental principles of protein folding etc.) and choice of appropriate prediction approach; basic principles and protocol of Homology Modeling; Databases of models; Basic principles for fold recognition, 1D profiles and threading approaches, basic principles of ab initio structure prediction and the broad approaches (what are the hierarchical and enumerative approaches, their general outline), Protein structure comparison and classification: classes, folds; the concepts in 3D structure comparison, purpose of structure comparison, algorithms such as FSSP, VAST and DALI Prediction of secondary structure based on energy consideration.

References:

  1. PCR PROTOCOLS - METHODS IN MOLECULAR BIOLOGY VOL 226 ,by JOHN MS BARTLETT / DAVID STIRLING
  2. HUMAN MOLECULAR BIOLOGY AN INTRODUCTION TO THE MOLECULAR BASIS OF HEALTH AND DESEASE , by RICHARD J EPSTEIN
  3. TEXTBOOK OF MOLECULAR BIOLOGY ,by SIVARAMA SASTRY K / PADMANABAN G / SUBRAMANYAM C
  4. CELL & MOLECULAR BIOLOGY ,by PETER J RUSSELL / STEPHEN L WOLFE / PAUL E HERTZ
  5. MOLECULAR BIOLOGY ,by ROBERT F WEAVER
  6. CELL & MOLECULAR BIOLOGY ,by PHILLIP SHEELER / DONALD E BIANCHI
  7. INTRODUCTION TO MOLECULAR BIOLOGY ,by PETER PAOLELLA
  8. MOLECULAR BIOTECHNOLOGY PRINCIPLES & APPLICATIONS OF RECOMBINANT DNA, by BERNARD R GLICK / JACK J PASTERNAK
  9. ANALYTICAL TOOLS FOR DNA GENES & GENOMES NUTS & BOLTS ,by ARSENI MARKOFF
  10. GENES & DNA A BEGINNERS GUIDE TO GENETICS & ITS APPLICATIONS ,by CHARLOTTE K OMOTO / PAUL F LURQUIN

PGDBI 1.2 Biostatistics

UNIT-1

Introduction to statistics, Data collection and presentation: Collection Classification, Tabulation and presentation of data. Experimental designs : Completely randomized block design (CRD), Randomised block design (RED), and Latin Square design (LSD)

UNIT-2

Measures of central tendency: Mean, Median, Mode. Measures of dispersion: Range, Mean deviation, Variance and Standard deviation. Hypothesis Testing: Errors level siqnificance, Tests based on student t , F and Chi-square (x2) , Analysis of Variance: one way and two way

UNIT-3

Probability: definition, Poisson and Normal distribution

Permutation and combinations Permutation and combinations

UNIT-4

Correlation and regression: Correlation, Correlation coefficient , Simple linear regression

PRACTICAL EXERCISES

Introduction to statistical software

MS Excel, SPSS, MINITAB, UNSCRAMBLER

References

  1. GENETICS & BIOSTATISTICS, MEYYAN RP,SARAS PUBLICATION, Edition:01,Year of Publication ,2009
  2. TEXTBOOK OF BIOSTATISTICS 1 – PB,SHARMA AK,DISCOVERY PUBLISHING HOUSE, Edition-01,Year of Publication,2005
  3. INTRODUCTION TO BIOSTATISTICS, GURUMANI N, ISBN978818094006 PublisherMJP PUBLISHERS , Edition 02, Year of Publication,2009
  4. INTRODUCTION TO BIOSTATISTICS & COMPUTER SCIENCE,SHAH YI / PARADKAR AR / DHAYAGUDE MG,NIRALI PRAKASHAN,Edition-11,Year of Publication, 2009
  5. BIOSTATISTICS FOR THE HEALTH SCIENCES, by CLIFFORD BLAIR R / RICHARD A TAYLOR
  6. ELEMENTS OF BIOSTATISTICS , PRASAD S,RASTOGI PUBLICATIONS, Edition02, Year of Publication,2009
  7. ZAR JERROLD.H, BIOSTATISTICAL ANALYSIS - 4TH EDI PEARSON EDUCATION ASIA
  8. Brain,W ,Biostatistics: Concepts and Application for Biologists. Chapman & Hall. London.
  9. Mahajan, B. K. Methods in Biostatistics Jaypee Brothers Medical Publishers. New Delhi.
  10. rao pss and Richard J An Introduction to Biostatistics.
  11. Gupta. S.P, Statistical methods, Sulthan chand and sons
  12. Ethance.D.N Fundamentals of statistics.

PGDBI 1.3 Data structure and Programming in C

UNIT-1

C Language Preliminaries Introduction, History and features of C, Characteristics of C, Applications of C. Constants And Variables, Fundamentals of C, Variables, Constants, Data Types, int, float, char, double. Input-Output statements, Formatted input, Formatted output statements, Unformatted input statements, Unformatted output statements

UNIT-2

Operators In C, C operators, unary operator, binary operator, arithmetic operator, increment operator, Decrement operator, relational operator, logical operator, bit wise operator, ternary Operator, comma operator, size of ()- operator, mathematical functions, header files, Preprocessor directives.

Control Statements, Conditional control statements, if-statements, if-else statements, nested if- statements, Switch-statements, go to statement. Loop Control Structures, While statement, do-while statement, for statement, nested for statement, break Statement, continued statement.

UNIT-3

Arrays, Definition, classification of arrays, declaration of an array, One-dimensional array & Multidimensional arrays. Functions Function definitions, arguments and parameters, category of functions, function with No arguments and no return values, function with arguments but no return value, Functions with no arguments and return values, local and global variables.Pointers, Definition, call by value and call by reference, pointer declaration, pointer notations. Strings, declaring and initializing string variables, reading and writing strings, string handling functions.

UNIT-4

Structures And Unions, Definitions, declarations, embedded structure declarations, initialization of a Structure, array of structures, unions, definitions, declarations, accessing union Members, initialization.

File operations, Data organization, file operations, opening a file, reading from a file, trouble in Opening a file, closing the file. Advanced concepts Bit fields, Marcos, types def.

Introduction to data structures, Stacks, Queues, and Linked lists, Trees, Conversions of expressions.

References :

  1. B.W.Kernighan and D.M.Ritchie C Programming Languages, 2/e, PHI
  2. P.B.Kotur Computer Concepts and C Programming Sapna Book House
  3. E.Balagurusamy, Programming in C, Tata McGraw Hill
  4. Yashavant P. Kanetkar Let us C BPB Publications
  5. V Rajaraman, Computer Basics and C, Tata McGraw Hill
  6. Gottfried, Programming With C, Sehaums Outline Series, Tata McGraw hill Publications

PGDBI 1.4 Introduction to Bio-informatics

UNIT-1

Bioinformatics- an overview, Definition and History, Applications of Bioinformatics. Introduction to Genomics, Introduction to Proteiomics. Sequence formats. Homology and similarity.Introduction to Data mining, NCBI, EBI, DDBJ, Database search software: ENTREZ, SRS, Expasy.

UNIT-2

Sequence Analysis, definition of sequence analysis, Nucleotide Sequence Analysis, Protein Sequence Analysis, Pair wise Alignment, global and local alignment, and significance of alignment, dot- plot.

Goals and types of alignment, Tools of sequence alignment, Homology sequence search, Parameters of Blast, BLAST2., BlastN, BlastP, tBlastX, TblastN BalstX, PSI Blast, Interpreting Blast Results, FASTA3.

UNIT-3

Multiple sequence analysis, Parameters of CLUSTAL-W, interpretation of Clustal W Out put, DNA Sequence Alignment, Protein Sequence alignment. Motif search.

Phylogenetic Analysis, Methods of phylogenetic analysis, Distance method, Parsimony Method, Maximum Likelihood Method, Types of Phylogenetic trees, Rooted tree, Un rooted Tree, Phylogram, Cladogram, , Clade.

UNIT-4

EMBOSS Introduction to emboss Software package

Reference:

  1. DAVID. W. MOUNT, BIOINFORMATICS SEQUENCE & GENOME ANALYSIS, COLD SERVING HARBOR LABORATORY
  2. BERGERON BRYAN, BIOINFORMATICS COMPUTING, PRENTICE HALL OF INDIA PRIVATE
  3. CLAVERIE JEAN-MICHAEL & NOTREDAME CEDRIC, BIOINFORMATICS - A BEGINNERS GUIDE, WILEY PUBLISHING INC,
  4. RASHIDI HOOMAN. M.S. & BACHELER LUKAS.K., BIOINFORMATICS BASICS - APPLICATI ON IN BIOLOGICAL SCIENCE, CRC PRESS
  5. ATTWOOD T.K. & PARRY SMITH D.J., INTRODUCTION TO BIOINFORMATICS, PEARSON EDUCATION.

PGDBI 1.5 Database and Biological Databases

UNIT- 1

Introduction to oracle:DBMS concepts, Data types, History of SQL, Advantages of oracle, DDL, DML, TCL and DCL commands, Query Processing and Concepts, Data Recovery, Primary and Secondary Index, Codd’s Rules,Operators: Union, Union all, Intersect, Minus, Comparison, Logical, Arithmetic. ER Diagram: One to One, One to Many, Many to One, Many to Many. Locking Concepts: Row level lock, Table level lock.

UNIT -2

Integrity Constraints: Domain Integrity Constraints, Entity Integrity Constraints, Referential Integrity Constraints. Database objects: Views, Sequences, Synonyms, Index. Functions: Group function, Single row functions

UNIT -3

Ms Access: Table, query, and relationshipPL/SQL: PL/SQL commands, Triggers, Procedures, Functions, Packages, Excerption and Error Handling. Security: Physical, Human, Operating System, Network, and Database.

UNIT -4

Introduction to Bioinformatics Databases, Importance of databases, Nucleic acid Sequence databases, NCBI, EBI, DDBJ. Protein Sequence Databases, UNIPROT, SWISS-PROT, PIR. Structure Databases, PDB. Bibliography Databases -PUBMED.

Secondary Databases.CATH, SCOP, PRODOM, PROSITE,

INTRODUCTION TO SEQUENCE SUBMISSION SOFWARES WEBIN, SEQIN, SAKURA.

GENOME DATABASES, PROTEIOMIC DATABASES. Metalobalomic Databases

REFERENCE

  1. ORACLE ESSENTIALS ORACLE 8 & ORACLE 8i, RICK GREENWALD / ROBERT STACKOWIAK / JONATHAN STERN, ISBN9788173661405, PublisherOREILLY, Edition,01 , Year of Publication-1999
  2. ORACLE 8 DESIGN TIPS AN ORACLE DESIGN, NA, OREILLY, ISBN978817366028X, Year of Publication-1997
  3. FUNDAMETALS OF DATABASE MANAGEMENT SYSTEMS, ALEXIS LEON / MATHEWS LEON,ISBN-9788182090296,Publisher,VIJAY NICOLE IMPRINTS PVT LTD,Year of Publication-2006.
  4. Henry F. Korth, Database System Concepts, Pearson Education.
  1. Bipin C. Desai, An Introduction To Database System, Galgotia Publications,
  2. Elemesri And S. Navathe, Fundamentals of Database System, Pearson Education.
  3. Leon & Leon. Database Management Systems, Vikas Publications.
  4. Michael Abbey & Michael J. Corey, Oracle A Beginners Guide, Tata McGraw Hill Publications

PGDBI 2.1 Tools of Bioinformatics

UNIT-1

Predictive methods using DNA sequences. Introduction to Bioinformatics software’s. Gene prediction Strategies. Gene prediction programs. ORF Mapping, CpG Plot, Primers, Primer Designing, Restriction Enzyme digestion, Expressed sequence tag,, SNP.

UNIT-2

Predictive methods using Protein sequences, Protein prediction strategies, Secondary structure prediction, Posttranslational modifications, Proteolytic enzyme digestion, helical wheel, and protein expression analysis. Identifying domains, Protein function prediction.

UNIT-3

All the analysis of Gene Tool, and Pep tool, PHYLIP Package All the softwares,All the analysis of Omega and D S GENE

UNIT-4

Introduction to Genome, Human genome project, Genomic, Structural Genomics, Functional Genomics, Pharmacogenomics.

REFERENCE

  1. Baxevanis & BFF Oluellette : Bioinformatics : A practical guide to the analysis of genes and proteins 2001 – AD – wiley Interscince – New York
  2. Stephen Misener & Stephan A. Krawetz, : Bioinformatics : Methods and Protocol – 2000 : Humana Press, New Jersey
  3. Des Higgins & willie tylore: Bioinformatics :Sequence, structure and databanks – 2000 : Oxford University Press
  1. David. W. Mount, Bioinformatics Sequence & Genome Analysis, Cold Serving Harbor Laboratory
  2. Bergeron Bryan, Bioinformatics Computing, Prentice Hall Of India Private

PGDBI 2.2 Object Oriented Programming in C++ and JAVA

UNIT-1

Classes and Objects Introduction, structures and classes, declaration of classes, member functions, defining the object of the class, accessing a member of class, array of class objects, pointer and classes, classes with classes (Nested class). Constructors, copy constructor, default constructor, Destructors, inline member Functions, Friend functions, Dynamic memory allocations, this pointer.Inheritance: Introductions, single inheritance, types of derivations, public inheritance, private

Inheritance, protected inheritance, array of class objects and single inheritance Multiple inheritance, multilevel inheritance, hybrid inheritance.

UNIT-2

Overloading: Function overloading, function overloading with various data types, function

Overloading with arguments, operator overloading, overloading assignment, Operator, overloading of binary operator, overloading arithmetic operator, Overloading of comparison operator, overloading of unary operator. Polymorphism, early binding, virtual functions, late binding, pure virtual Functions, abstract base classes, virtual base classes.

UNIT-3

Introduction to Java and its Features: Introduction to object oriented paradigm, Concepts of Object-Oriented programming (Objects and Classes, Data abstraction and encapsulation, inheritance, polymorphism, Dynamic binding).Basics of Java: Java history; Java features (Compiled and interpreted, Platform-independent and portable, Object-Oriented, Robust and Secure, Distributed, Simple, Small and Familiar, Multithreaded and interactive, High performance, Dynamic and extensible); How Java differs from C and C++.

UNIT- 4

Classes ,Objects and Methods: Introduction, Defining a class, adding variables and methods, creating objects, accessing class members, constructors, method overloading and overriding, this keyword, finalize() and garbage collection, inheritance and abstract classes.Packages: Introduction, Java API packages, using system packages, naming conventions, creating packages, accessing a package, using a package, adding a class to a package

References:

  1. Herbert Schildt, C++ The Complete Reference, Tata McGraw Hill Publication.
  2. Paul S. Wang, Standard C++ with Object Oriented Programming, Thomson Learning.
  3. E. Balagurusamy, C++, Tata McGraw Hill Publication.
  4. B. A. Forouzon, R. F. Gilberge, Computer Science: A Structured Approach Using C++, 2/e, Thomson Learning.
  5. Java2- All-in-one, Boone Barry and Stanek William, The Mcgraw-Hill Company, 2000, New Delhi
  6. Java- How to program, Deitel and Deitel, Prentice-Hall, 2000, New Jersey.
  7. Programming with Java- Balaguruswamy
  8. The Complete Reference Java 2-Schildt Herbert
  9. The java Programming Language- Arnold Ken

PGDSD 2.3 Web and Networking technologies

UNIT – 1

Networking: Needs and Advantages, Network, Network Types – Client, Server and Peers, introduction to various types of servers. TCP / IP reference Model and ISO reference Model, Physical layer, Data link layer, MAC (Medium Access Control) and LLC (Logical Link Control), Error Detection and Correction.

Network topology – Bus, Star, Ring, Star bus, Star ring, Mesh, features, Advantages and Disadvantages of each type. Transmission media – Guided transmission media, unguided transmission media.

UNIT – 2

LAN standard, 802.3,802.4,802.5, Ethernet, Fast Ethernet, Token Rings, FDDI, ATM , Network layer: circuit switching, packet switching, routing and congestion control. Transport layer, connection oriented service, connectionless oriented service, TCP and UDP.

UNIT – 3

Value Added Networks: X.25 Interface Network, Frame Relay, ISDN (Integrated Service Digital Network. Interface Devices, Application Layer: Email, WWW, and FTP. Network Security, Satellite communication.

UNIT – 4

Web Designing [HTML]: HTML and its features, Document Structure Elements, Text Formatting Elements, Block Formatting Elements, Hyperlinks, Marquee, Lists, Table, Forms, Frames, Graphics, Image Mapping, HTML and Multimedia .CSS.

Practical Exercise

Crimping RJ45 Connectors, Installation of switch, TCP/IP configuration, Pinging and Checking, Net meeting: configuration, chatting, whiteboard, File Transfer, Desktop sharing, Application sharing, Installation of web camera and web chat, Net meeting conference, installation of printer, printer sharing. Web Designing [HTML]:

Reference:

  1. Andrew & Tanenbaum, Computer Networks, Pearson Education.
  2. William Stallings, Data and Computer Communications, 7/e Pearson Education.
  3. S.K Basandra & S.Jaiswal, Local Area Networks, Galgotia Publications.
  4. Ames Chellis Charles Perkins, Mathew Strebe Networking Essentials: Study Guide MCSE, 2/e, BPB Publication.
  5. Black Uyless, Computer Networks: Protocols, Standards, and Interfaces, 2/e, PHI.
  6. William A Shay, Understanding Communications and Networks, 3/e, Thomson Learning – Vikas Publication.
  7. World Wide Web Design with HTML- Xavier
  8. Web Technology – Sharp Series

PGDBI 2.4 PROJECT

Elective Paper

PGDBI –E-1 Proteomics and Drug Designing

UNIT-1

Introduction to protein structure, Protein Structure prediction, Intrinsic Tendency Of Amino Acids To Form  Turns. Molecular Visualization, Pdb File Format, RASMOL Display Styles Wire Frame , Ball And Stick, Space Fill, Ribbons, Cartoons. RASTOP CN3D.Molecular modeling, Construction of initial model, Refining the Model, Manipulating the model, Rotomer libraries, Three- Dimensional structure prediction, comparative modeling, Homology modeling, Threading, Energy based prediction of protein structures, Modeling softwares SPDBV. SWISS-Model. Introduction To Simulation And Modelling Soft Wares On The Pdb.

UNIT-2

Introduction to basic concepts, Molecular recognition by receptor and ligand design, Genaration of Rational Approaches in Drug design, Introduction to drug designing, Discovering a drug, Target identification and validation, Identifying the lead compound, Optimization of lead compound,

UNIT-3

Docking methods introduction, three dimensional description of binding site environment and Energy calculation, Automatic Docking Method, Three Dimensional database search Approaches, Automated structure Construction methods, . AUTODOCK, Argos Lab,

UNIT-4

Micro array technology, Basics of Biochips and Microarray Technology, Historical Development, Biochip. DNA Micoarrays, Ologonucleotide, cDNA, and Genomic Microarrays. Application of microarray. Commercial aspects of Microarray technology.DS VIEWER

References

  1. PROTEOMICS FROM PROTEIN SEQUENCE TO FUNCTION ,by ENNINGTON SR 0 / DUNN MJ
  1. PROTEOMICS FROM PROTEIN SEQUENCE TO FUNCTION , by PENNINGTON SR
  2. PURIFYING PROTEINS FOR PROTEOMICS A LABORATORY MANUAL ,by RICHARD J SIMPSON
  3. DISCOVERING GENOMICS PROTEOMICS & BIOINFORMATICS ,by MALCOLM CAMPBELL / LAURIE J HEYER
  1. GUIDEBOOK ON MOLECULAR DRUG DESIGN ,by CLAUDE COHEN N
  2. MOLECULAR MODELLING & DRUG DESIGN,by ANAND SOLOMON K
  3. DRUG DESIGN ,by MORRIS SYLVIN
  4. INTRODUCTION TO DRUG DESIGN ,by PANDEYA SN / DIMMOCK JR
  5. COMPUTER AIDED DRUG DESIGN METHODS & APPLICATIONS ,by THOMAS J PERUN / PROPST CL
  6. TEXTBOOK OF DRUG DESIGN & DISCOVERY ,by POVL KROGSGAARD LARSEN / TOMMY LILJEFORS / ULF MADSEN
  7. Clude Cohen, The molecular modeling perspective in drug design, Acedemic press
  8. Branden C, and Tooze R Introduction to protein Structure
  9. Creighton T.E., Proteins, Freeman W.H
  10. Grigorenko, E.V DNA ARRAYS Technology and Experimental Stratergies CRC press

PGDBI-E-2 Comparative genomics