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DETAILED SYLLABUS


FOR


DISTANCE EDUCATION




PGD( Bioinformatcis
)


(SEMESTER SYSTEM)










PGD BIOINFORMATICS


COURSE TIILE

: PGD BIOINFORMATCIS


DURATION

: 04 Semesters


TOTAL MARKS

: 900



FIRST SEMESTER

COURSE TITLE

Paper Code


MARKS

THEORY

PRACTICAL

TOTAL

Introduction To Bioinformatics

PGDBI
-
S110

100

00

100

Molecul
ar Biology

PGDBI
-
S120

100

00

100

Computational Skills For
Bioinformatics

PGDBI
-
S130

100

00

100

Sequence And Phylogenetic
Analysis

PGDBI
-
S140

100

00

100

Genomics, Proteomics and other
Bioinformatics applications

PGDBI
-
S150

100

00

100


SECOND SEMESTER


COURSE TITLE

Paper Code


MARKS

THEORY

PRACTICAL

TOTAL

The Cell

PGDBI
-
S210

100

00

100

Genetic Engineering

PGDBI
-
S220

100

00

100

Enzyme and Protein Synthesis

PGDBI
-
S230

100

00

100

Structure prediction and Bio
Energetics

PGDBI
-
S240

100

0
0

100















PGD BIOINFORMATICS



FIRST SEMESTER


Introduction To Bioinformatics

Course Code:PGDBI
-
S110

BioInformatics: An Overview

Introduction

Objectives Of Bioinformatics

What Kind Of Data Is Used

Multiplicity Of Data And Redundancy

Major Bioin
formatics Databases

Data Integration

Data Analysis

Careers In Bioinformatics

Reference List Of The Major Bioinfomatics Databases And Tools


Molecular Biology And Bioinformatics


What Is Molecular Biology

Systems Approach In Biology

Central Dogma Of Molecul
ar Biology

Important Definitions Related To Central Dogma

Problems In Molecular Approach And The Bioinformatics Approach

Overview Of Bioinformatics Applications

















Molecular Biology

Course Code:PGDBI
-
S120


The Information Molecules And Inform
ation Flow

Introduction

Basic Components

Basic Chemistry Of Nucleic Acids

Structure Of DNA

Structure Of RNA

DNA Replication Is Semi
-

Conservative

Denaturation And Renaturation Of DNA

Genes
-
The Functional Elements In DNA

Organization Of Genes In Eukaryotic
Chromosomes

Structure Of Bacterial Chromosome

Analyzing DNA

Closing Methodology

DNA Sequencing And Polymerase Chain Reaction(PC)


Proteins
-
Their Structural Profiles And Properties


Introduction

Amino Acids

Protein Structure

Secondary Structure Elements

Te
rtiary Structure

Quaternary Structure

Protein Folding

Protein Function

Proteins
-
Purification And Characterisation,













Computational Skills For Bioinformatics

Course Code:PGDBI
-
S130


Using The Linux Operating System


Introduction To Linux

The Bas
ics Of Linux System

Using Linux File System And Directories

Text Processing

Writing Shell Programs


Progaramming With Perl

Introduction To Peal

Programming In Peal

Illustrations Of Programming In Peal

Operation With Associative Arrays (Hashes)

File Input A
nd Output

Peal Application For Bioinformatics,

Peal Application For Bioinformatics
-
Bioperl

Other Related Projects


Understanding And Using Biological Databases


Introduction

Types Of Databases

Networks And Databases

Introduction To The Java Clients

Corba
-
C
ommon Object Request Broker Architecture

Using Mysql

Introduction To Biostatistics,








Sequence And Phylogenetic Analysis

Course Code:PGDBI
-
S140


Alignment Of Pairs Of Sequence

Introduction To Pairs Of Sequence

Sequence Analysis Of Biological Data

Mod
els For Sequence Analysis And Their Biological Motivation

Methods Of Alignment

Application Of Dot Matrices

Methods For Optimal Alignments

Using Gap Penalties And Scoring Matrices

Sensitivity And Specificity

Illustrative Examples


Tools For Sequence Alignme
nt

Introduction

FAST

Blast

Filtering And Gapped Blast

PSI
-
Blast

Comparison Of Running Time For Various Programs

Alignment Of Multiple Sequences

Introduction

Tools For MSA

Considerations In Conducting MSA,

Application Of Multiple Alignment

Viewing MSA

Sequ
ence Detection Efficiency Measures:Sensitivity And Specificity

Phylogenetic Analysis

Introduction

Concept Of Trees

Phylogenetic Trees And Multiple Alignments

Distance Matrix Methods (MD)

Character Based Methods

Methods Of Evaluating Phylogenies

Summary Of
The Phylogenetic Methods

Steps In Constructing Alignments And Phylogenies

Considerations In Choice Of The Method

Working With Phylogenetic Trees
-
An Illustration


Genomics, Proteomics and other
Bioinformatics applications

Course Code:PGDBI
-
S150


Gene Predi
ction

Introduction

Using Patterns To Predict Geges

Methods Of Gene Prediction Tools

Summary Of Tools For DNA/RNA Structure And Function Analysis


Visualization And Prediction Of Protein Structure

Protein Structure Overview

Different Structure Proteins,


P
rotein Structure Databases And Visualization Tools

Protein Classification

Protein Structure Prediction For Known Folds

Methods Of Structure Prediction For Unknown Folds

Protein Function Prediction

Accuracy Of Prediction



Gene Mapping,Sequence Assembly And

Gene Expression


Introduction

Gene Mapping

Application Of Mapping

DNA Sequencing

Algorithm For Alignment Of Sequencing Fragments

DNA Microarrays,

Microarray Experiment Design And Data Analysis


Proteomics

Introduction To Proteomics

Proteome Analysis

Tools

For Proteome Analysis

Metabolic Pathways

Genetic Networks

Network Properties And Analysis

Complete Pathway Simulation:E
-
Cell




Problem Solving In Bioinformatics


Introduction

Genomic Analysis For DNA Sequences

Genomic Analysis For Protein Sequences

Strat
egies And Options For Similarity Search

Practical Considerations In Sequence Analysis

Flowchart For Protein Structure Prediction

































SECOND SEMESTER


The Cell

Course Code:PGDBI
-
S210


Cell

History, Gross Morphology of the Cell,
Cell wall, Ultra Structure of the cell
wall, Plasma membrane, Chemical composition, membrane Functions,
membrane models, Cytoplasm, Nucleus, Nucleolus, Nucleic Acids,
Molecular model of DNA Structure, Replication of DNA, replication in
Circular DNA, Types
of RNA, Mitochondria , Chloroplasts, Chlorophylls,
Bio Synthesis of Chlorophylls, Carotenoids, Endo Plasmic Reticulum,
Ribosomes, Golgi Complex, Lysosomes, Centrosomes, Microbodies.

Bio Molecules

Carbohydrates ,Fats and Proteins

Nucleic Acids

Bacterio phag
es and Chemical basis of heredity, Nucleic Acids, DNA,
Chemical Composition, Molecular Model,Alternative Forms of DNA
Helices, RNA, Molecular Structure, Types of RNA.



Genetic Engineering

Course Code:PGDBI
-
S220


Outline Procedure of genetic Engineering,

Restriction Enzyme, Isolation of
Gene, Shotgun Method, Obtaining DNA from RNA, Vectors Plasmids,
Bacterio phages, Cosmids, Phasmids, Cloning organisms, Techniques use
for Identification of Clone, Polyacrylamide gel Electrophoresis, PFGE,
Southern blotting

Technique, Northern and Western blotting Techniques,
Construction of Chimeric DNA,Cohesive End,dA
-
dT tailing, blint End
Litigation, cDNA Liabraries, Transfer of recoPGDBInant DNA into Cloning
organisms, Expression of Cloned DNA, Applications of Genetic
E
ngineering, Scope
-
nif
Genes
,
Genetically Engineered Insulin,Human
growth hormone, Vaccine of Rabies Virus, Biohazards and safeguards of
genetic Engineering.







Enzyme and Protein Synthesis

Course Code:PGDBI
-
S230

Protein Synthesis



Protein Structure and C
lassification



The Central Dogma



Wobble Hypothesis



Initiation of Polypeptide Protein Chain



Chain Elongation



Chain Termination

Gene Expression

Induction and Repression, The operon Concept, types of Regularity
Mechanism, Negative Control, Positive Control,
Catabolic Expression,
Feedback Inhibition
-
the lac operon, The gal operon, Tryptophan Operon,
Arbinose operon, gal gene in Yeasts, regulation of transcription in Phage
DNA, genetic Regulation in Eukaryotes.

Enzymes

Structure and Chemical composition, Distri
bution of Enzymes in Plant Cells,
Nomenclature and Classification, Properties of Enzymes, Mechanism,
Enzyme Kinetics, Models for Enzyme Action, Lock and Key Model,
Induced fit, Allosteric Regulation, Double replacement(ping pong) reaction,
Factors affectin
g Enzyme Action.


Structure Prediction and Bio energetics

Course Code:PGDBI
-
S240


Bio Energetics

Energy and matter,types of energy, Laws of thermodynamics, first
law,Second Law ,Concept of free energy, Calculation of Standard free
energy, Energy change.

B
asic Computing for Biologists

Computational Definitions

The CPU

Operating systems

Computer networks

Protein Structure Prediction

Secondary Structure Prediction, Chou
-
fasman, Jpred, Q
3
,transmembrane
protein Prediction, Tertiary Structure predication, Compa
rative Modelling,
Fold recognition, Ab initio Prediction, Modeller, RASMOL.