Part I & Part II - Punjabi University Patiala

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Proposed
Syllabus

M.Sc. Bioinformatics

(I, II, III & IVth Semesters)

2009
-
11 Sessions



The course

will consist of four Semesters i.e. two semesters in one year. N each semester
there shall be four theory papers and four practical papers.

Each theory pape
r shall be of 100 marks of which 80 marks shall be allocated to theory
paper set by external examiner. The Internal assessment in each paper shall have 20
marks. There shall be one assignment of 5 marks, one test of 10 marks (best of two shall
be taken) an
d 5 marks of seminar.

The awards of internal assessment shall be dispatched by the Head of the Department
before the commencement of semester examinations. The seminar will be allotted to all
the students from the respective syllabi of theory papers in suc
h a way that each student
could be assessed by the teacher of the subject.

The Subjects and distribution of marks shall be as under:



M.Sc. Bioinformatics


Semester
-
I

Theory papers:

Paper
-
I


Basic Mathematics and Statistics/ Fundamentals of Biology 10
0 marks
Paper
-
II


Concepts in Computers and SQL



100 marks

Paper
-
III


Introduction to Bioinformatics and Biodiversity

100 marks

Paper
-
IV


Biological Chem
istry





100 marks

Practical papers:

P
ractical Paper
-
I

Pertaining to T
heory

Paper
-
I

& II


100 marks

Practical Paper
-
I
I

Pertaining to T
heory

Paper
-
I
II & IV


100 marks




Semester
-
II

Theory papers:

Paper
-
V

Chemo informati
cs and Drug Designing


100 marks

Paper
-
VI

Molecular Modeling





100 marks

Paper
-
VII

Computational Biology




100 marks

Paper
-
VIII Immunote
chnology and Biochemical Techniques

100 marks

Practical papers:

P
ractical Paper
-
III

Pertaining to T
heory

Paper
-
V & VI


100 marks

Practical Paper
-
IV

Pertaining to T
heory

Paper
-
VII & VIII

100 marks








Semester
-
III

The
ory papers:

PaperIX Programming in C++ and PERL



100 marks

PaperX Advanced Computer Programming



100 marks

Paper
-
XI

Genomics and Proteomics




100 marks


PaperXII

Functional Genomics





100 marks

Practical papers:

P
ractical Paper
-
V

Pertaining to T
heory

Paper
-
I
X & X


100 marks

Practical Paper
-
VI

Pertaining to T
heory

Paper
-
XI & XII


100 mar
ks





Semester
-
IV

Theory papers:

Paper
-
XIII

Java Programming and Data mining



100 marks

Paper
-
XIV

Numerical Methods and Optimization Techniques

100 marks






Practical papers:


P
ractical Paper
-
VII

Pertaining to T
heory

Paper
-
XII
I

& XIV

100 marks







Project Work; in plant Training, Seminar and industrial Visit


Satisfactory/Unsatisfactory


Project Work
shall be evaluated by two external examiners Satisfactory or
Unsatisfactory. After the evaluation, two examiners will conduct Viva Voce examination.
Seminar on project will be evaluated by team of three teachers. The awards of Seminar
and industrial visits

shall be communicated by the Head of the Department/ Principal
before the commencement of the exams. Unsatisfactory will be considered as fail.



















Semester
-
I

Paper
-
I:
Basic Mathematics and Statistics

Max Marks: 80






Lectures to be delive
red: 60

Time allowed: 3 Hours





Pass Marks: 35%


The Question Paper will consist of five sections A, B, C, D, and E. Section A, B, C
and D will have two questions from the respective sections of the syllabus and carry
15 marks each. Section
-
E consist of
10 short answer type questions which will cover
the entire syllabus uniformly and will carry 20 marks in all

.

Section A

Matrices, Limit: Limits of function

Differentiation: Rules for differentiation, Calculation Gradients of chords of first and
higher ord
er derivatives, Applications, Increasing and Decreasing functions, Maximum
and Minimum points.


Section
B


Integration: Basic rules for integration, Integration by parts, Definite and non definite
integral, Logarithms, Ordinary differential equations (firs
t order), Partial fraction,
Substitution methods for definite integral, Calculating areas.

Boolean Logic: Addition, Subtraction, Multiplication and Division using Binary, Octal
and Hexadecimal systems.


Section
C


Elementary Statistics: Continuous frequenc
y distribution, Graphic representations of a
frequency distribution, Histogram, Frequency polygon, Measures of central tendencies
-

Mean, Mode, Median.

Regression and correlation: Scatter diagrams, Regression functions, linear correlation and
regression lin
es, Product moment, Correlation Coefficient.



Section
D


Probability: Experimental probability, Probability when outcomes are equally likely,
subjective probabilities, probabilities law, probability and independent events, Bayes’s
theorem.

Distribution: B
ernoulli distribution, Binomial distribution, Poisson distribution and
Normal distribution, Tests of significance.


Suggested Readings:

1.

H. Nell and D.Quadling, “Pure Mathematics Vol. 1, 2, 3. Cambridge University
Press. 2002.

2.

Edward Batschelet, “Introducti
on to Mathematics for Life Scientists”. 3
rd

Edition,
Melson Thomes, 2002.

3.

J. Crawshaw and J. Chamber, “Advanced Level Statistics”. 4
th

Edition, Melson
Thomees, 2002.


Paper
-
I: Fundamentals of Biology

Max Marks: 80






Lectures to be delivered: 60

Time al
lowed: 3 Hours





Pass Marks: 35%


The Question Paper will consist of five sections A, B, C, D, and E. Section A, B, C
and D will have two questions from the respective sections of the syllabus and carry
15 marks each. Section
-
E consist of 10 short answer

type questions which will cover
the entire syllabus uniformly and will carry 20 marks in all


Section
-
A

Introduction to Life science: Origin of life, Unicellularity and multicellularity,
prokaryotes and eukaryotes, Systematic and Classification.

Nutrition

in animals: Introduction to digestive system of human, Digestive glands, Types
of nutrition, Mechanism of digestion, Nervous and hormonal control of digestive
secretion.

Transport in animals: General character of Blood vascular system, System in animals,
Composition of blood and lymph, Mechanism of transport, functions of blood and lymph.


Section
-
B

Coordination and Control in animals: Nervous system
-

parts of nervous system,
secondary receptors, structure and functions of receptors, Endocrine system
-

Intr
oduction, Study of behavior: Innate and Learned.

Heredity and variation: Mendel work, Chromosomal basis of inheritance, Linkage, Gene
interaction, Gene mapping, Mutations.

Reproduction
-

sexual reproduction, review of sexual reproduction in human, human
rep
roductive system.


Section
-
C

Plant
Classification: Salient features of Be them and Hookers, Hutchinson and Engler
criteria for primitive and advanced nature of families and flower, Bryophyte, Lichen,
Gymnosperm, Angiosperms
-

General characters, Taxonomic i
mportance of floral parts.


Nutrition in Plants: Autotrophic nutrition Introduction to photosynthesis, mechanism of
photosynthesis, factors affecting photosynthesis, Metabolism of glycerate phosphate and
trios phosphate pathways.

Ecology
-

ecosystem, ener
gy flow, community ecology, factor influencing environment &
habitat.


Section
-
D

Coordination and control in Plants: Plant movement, Plant growth hormones, Synergism
and antagonism, phytochrome and effect of light of plant development verbalization and
flo
wering.


Transport in Plants: plant water relation, movements of water through the growing plants,
transpiration and movement of water through the lead, ascent of sap, Xylem and phloem:
Structure and function, mechanism of transport of minerals and water.

Secondary growth in stem & roots of helianthus, Boerhavia.


Suggested Readings:


1.

Biological Science by Taylor J.D.Green O.P.N. Stout W.S.

2.

Lehninger Principles of Biochemistry by David L. Nelson, Michel Cox.

3.

Fundamentals of Biochemistry by J.L. Jain and S.C
hand & Co. Ltd.

4.

Harper Biochemistry by R.K.Murry. P.A. Nagar, D.K. Granner, P.A. Mayer
(2000), Prentice hall International.





Paper
-
I
I
: Concepts in Computers and SQL

Max Marks: 80






Lectures to be delivered: 60

Time allowed: 3 Hours





Pass Marks: 35
%


The Question Paper will consist of five sections A, B, C, D, and E. Section A, B, C
and D will have two questions from the respective sections of the syllabus and carry
15 marks each. Section
-
E consists of 10 short answer type questions which will cover

the entire syllabus uniformly and will carry 15 marks in all.


Section A


Computer Fundamentals: Historical evolution of computers, Characteristics of
computers ,

capabilities and limitations of computers , computer generations,
classification of compute
rs (PCs, micro, mini, miniframe, supercomputers ) comparison
with memory, power, cost ,size then and now.

Block diagram of computer, identifying various components and their functions, primary
storage: concept of RAM, ROM, and EPROM etc.

Secondary Memory
: magnetic tapes and disk, hard disk, floppy disk, compact disk and
CD
-
ROM

I/O devices: keyboard, tape/disk/diskette, light pen, mouse, joystick, printer, plotter,
voice report system.




Section
-

B


Operating system: Need of OS, its functions, functions o
f common used operating
system: Windows, Linux

Computer networking
-

types of computer networking: LAN, WAN, MAN, Network
topologies, network goals, TCP/IP protocols, Network securities.


Section
-
C


Multimedia database

basic concepts and applications.

Inde
xing and Hashing, Text database.

Introduction to distributed database primary


Section
-
D


Introduction to database, Entity set, ER model, Network model and Hierarchical model,
Relational model.


SQL

Select statements;

Data definition statements
,
Data mani
pulation statements
,
Data control
statements

Other database objects (Views, Sequences, and Synonyms)
,
DDL table: create, alter, and
drop
,
DML: Record, insert, delete, update and truncate
,
Keys: primary, foreign, unique,
check, default, candidate, alternate
.


Suggested readings:



1.

V. Rajaraman, “
F
undamentals of computers” (2
nd
edition), Prentice Hall of India,
New Delhi, 1996.

2.

B.Ram, “computer fundamentals”, Wiley, 1997.

3.

Programming in C by Balagurusami
.

4.

let us C by Yaswant Kanitkar
.

5.

An introduction to databa
se system by C J Date Pearson Education

6.

Oracle SQL complete Reference by Tata McGraw Hill













Paper
-
III: Introduction to Bioinformatics and Biodiversity

Max Marks: 80






Lectures to be delivered: 60

Time allowed: 3 Hours





Pass Marks: 35%


The

Question Paper will consist of five sections A, B, C, D, and E. Section A, B, C
and D will have two questions from the respective sections of the syllabus and carry
15 marks each. Section
-
E consist of 10 short answer type questions which will cover
the en
tire syllabus uniformly and will carry 20 marks in all


Section
-
A

Introduction to Bioinformatics: What is Bioinformatics, its goals and scopes, Application
of Bioinformatics, Human Genome Project, Role of Computers and Biology in
Bioinformatics.

Introducti
on to Biological Databases: Characteristics and Classification of Databases
-

Primary, secondary , Composite and Specialised Databases.

ENTREZ, EBI, NCBI, ExPasy

File Formats: FASTA, ASN.1, GenBank, EMBL, ClustalW

, PHYLIP.


Section
-
B

Sequence Analysis:

Pa
irwise alignment: Global alignment and Needleman Wunsch Algorithm, Local
alignment and Gap penalty and its Statistical significance

Scoring Matrices: PAM, BLOSUM.

Sequence alignment methods: Dot Matrix, Dynamic Programming, k
-
Tupple method

Multiple sequenc
e alignment: Exhaustive and Heuristic algorithms, Position Specific
Scoring Matrices, Hidden Markov Model, applications of multiple sequence alignment

CLUSTALW, CLUSTALX, T
-
Coffee.


Section
-
C

Database similarity searching: Heuristic Database searching, BLA
ST: algorithm and
versions, FASTA, Comparison of BLAST and FASTA.

Molecular phylogenetic : Molecular evolution and Phylogenetics, Terminology of
Phylogenetic Trees: Branches. Nodes, Clade, Taxa, OUT, Rooted and Unrooted tree.

Forms of Tree representation:
Phylogram. Cladogram. Dedrogram.

Phylogenetic tree construction methods: Distance and character based methods,

Phylogenetic Tree evaluation: Bootstrapping (Parametric and Non
-
parametric), Jack
knifing,


Section
-
D

Biological Diversity: Species Biodiversity
-
taxonomic information on plants, animals,
viruses and microbes; Genetic diversity; Ecosystem Diversity, speciation and Modes of
Speciation, Methods of Species identification and classification, Tree Of Life.

Dataset in Biodiversity informatics: Species200
0, Tree of Life, ATCC, ICTV, Animal
Virus Information system.



Suggested Readings:

1.

Essential Bioinformatics by Jin Xiong.

2.

Bioinformatics : Sequence and Genome Analysis by David W. Mount.

3.

Bionformatics: Concepts, Skills and applications by R. C. Rastogi.

4.

I
ntroduction to Bioinformatics by Singhal and Singhal.

5.

Bionformatics: A Practical Guide to analysis of Genes and Genomes by Andreas
D. Baxevanis and b. F. Francis Ouellette.

6.

Bioinformatics Basics by Hooman H. Rashidi, Lukas K Buehler.

7.

Bioinformatics: A mode
rn approach by Vittal R. Srinivas.

8.

Bioinformatics: Database and Systems by Stanley Latovsky.

9.

Biodiversity by Perlman.

10.

Biodiver
sity: an Introduction by Gaston.






Paper
-
IV: Biological Chemistry

Max Marks: 80






Lectures to be delivered: 60

Time allowed:

3 Hours





Pass Marks: 35%


The Question Paper will consist of five sections A, B, C, D, and E. Section A, B, C
and D will have two questions from the respective sections of the syllabus and carry
15 marks each. Section
-
E consist of 10 short answer type
questions which will cover
the entire syllabus uniformly and will carry 20 marks in all
.


Section
-
A

Water as Universal biological solvent, concept of osmolarity.

Proteins: amino acids and peptides; primary, secondary tertiary and quaternary structures;
str
ucture function and evolutionary relationships; Protein folding, Molecular chaperons,
GroEL/GroEs system.

Section
-
B

Enzymes: details of enzyme nomenclature and classification, coenzymes, and metal
cofactors, temperature and pH effects; Michaelis menten kin
etics, inhibitors and
activators; active site and catalytic mechanism; Isoenzymes; osmolytes and Intracellular
modulation of enzymes.

Organization of metabolic system: Enzyme chains, Multienzyme complexes and
multifunctional enzymes; Anaplerotic sequences
and Amphibolic pathways; Pacemaker
enzymes and feedback control of metabolic pathways; Shuttle Pathways and energy
changes.


Section
-
C

Carbohydrates: Monosaccharides, Oligosaccharides, Polysaccharides, Proteoglycans and
Glycoproteins.

Carbohydrate Metaboli
sm: Biosynthesis and Degradation of Carbohydrates, feed
pathway of Glycolysis, Krebs Cycle: Enzymes of Krebs cycle, amphibolic nature of
Krebs cycle, regulation of Carbohydrate metabolism, Electron Transport and Oxidative
Phosphorylation, Mitochondrial Ele
ctron Transport Chain, Oxidative phosphorylation
Regulation of ATP synthesis


Section
-
D

Lipids: Fatty acids, acylglycerols, phospholipids, sphingolipids, cholesterol and
membranes, isoprenoids, eicosanoids and their biological importance.

Lipid Metabolism:

Biosynthesis and Degradation of Fatty acids, Metabolism of
triacylglycerols, Cholesterol metabolism.

Nitrogen Metabolism: Reduction and assimilation of atmospheric nitrogen, Biosynthesis
and degradation of amino acids, amino acids as precursors of heme, b
iosynthesis and
degradation of nucleic acids.



Suggested Readings:

1.

Biochemistry by Victor L. Davidson, Donald B. Sittman.

2.

Lehninger: Principles of Biochemistry by David L. Nelson, Michel Cox.

3.

Fundamentals of Biochemistry, J.L. Jain, S. Jainand N. Jain, S.

Chand & Co. Ltd.

4.

Biochemistry by Dawn B Marks.





Practical Paper
-
I

Pertaining to Theory Paper
-
I

& II



10
0 marks


Basic Mathematics and Statistics

1.

Convert Binary to Hexadecimal.

2.

Convert Binary to Octal.

3.

Draw the Frequency Distribution Curves with Histog
ram on EXL SHEET.

4.

Computation of Mean, Variance and Standard deviation using given data.

5.

Computation of MODE using given data.

6.

Computation of MEDIAN using given data.

7.

Find the Bernoulli distribution using the given data.

8.

Find the Binomial distribution usin
g the given data.

9.

Find the Poisson distribution using the given data.

10.

Find the normal distribution using the given data.


Concepts in Computers and SQL


1.

MS Office
.

2.

Creating database in SQL.

3.

Performing all types of statements of SQL.




OR



Practical Paper
-
I

Pertaining to Theory Paper
-
I



10
0 marks

Fundamentals of Biology



1.

V.S of mammalian Skins, T.S. of Testis, Ovary, Lungs, Pancreas, Kideny,
Deudenum, Spleen, Large Intestine, Artery, Vein, Uterus, Spleen.

2.

Microtomay (Instrumentation detail)

3.

Electron Micr
oscope. (Study).

4.

Compound Microscope(study)

5.

Determination of Blood groups in humans (A, B, AB, O).

6.

Hb% content in blood (HUMAN)

7.

Root tip different stages of mitosis in root tip.

8.

Models DNA, RNA Kidney, Eye, Lungs,

Heart, Female reproductive system,
Male re
productive system.

9.

Section cutting of root.

10.

Section cutting of leaves.


Concepts in Computers and SQL


1.
MS Office
.

2. Creating database in SQL.


3. Performing all types of statements of SQL.




P
ractical Paper
-
I
I

Pertaining to Theory Paper
-
I
II & IV


10
0 marks

Introduction to Bioinformatics and Biodiversity


1.

Explore NCBI.

2.

To explore Expasy:Swiss Prot.

3.

To explore EBI

4.

Working on search engines:ENTREZ and SRS.

5.

Perform local alignment using all BLAST versions.

6.

Perform multilple sequence alignment using Cl
ustalW.

7.

Perform multilple sequence alignment using T Coffee.

8.

Show the phylogenetic analysis by PHYLIP.

9.

Phylogenetic analysis by MEGA.



Biological Chemistry


1.

Quantitative estimation of Carbohydrate.

2.

Identification of given Lipids.

3.

Estimation of fat va
lue of given fat sample.

4.

Quantification of protein by TLC.

5.

Quantitative estimation of protein by Bradford method.

6.

Quantitative estimation of protein by Lowery method.

7.

Quantitative estimation of protein by Biuret method.

8.

DNS method.

9.

Extraction of casein fro
m Milk.

10.

Gel electrophoresis.









































Semester
-
II


Paper
-
V: Chemo informatics and Drug Designing

Max Marks: 80






Lectures to be delivered: 60

Time allowed: 3 Hours





Pass Marks: 35%


The Question Paper will consist of f
ive sections A, B, C, D, and E. Section A, B, C
and D will have two questions from the respective sections of the syllabus and carry
15 marks each. Section
-
E consist of 10 short answer type questions which will cover
the entire syllabus uniformly and will
carry 20 marks in all


Section A


Introduction to Drug Designing: Process of Drug discovery, Drug designing approaches:
Target based, Ligand based and De Novo Drug Designing.

Pharmacophore deduction and modeling,

Analysis and Design of Combinatorial
Libra
ries
, Drug receptor interactions,

Section B

Representation and Manipulation of 2
-
D Molecular Structures: Introduction, Computer
representation of Chemical Structures, Structure Searching, Substructure searching,
Reaction Databases, representation of Patent
s and Patent Databases,
3
-
D Pharmacophores
and Methods to derive 3D Pharmacophores.



Section C

Basic principles of Docking, Virtual Screening: Introduction, Structure Based Virtual
Screening
-

Protein Ligand Docking, Scoring Functions for Protein Ligand do
cking,
Practical aspects of structure based Virtual Screening; Prediction of ADMET Properties,
2 D and 3D data searching, Chemical databases, Role of computers in Chemical
Research.




Section D

QSAR: Basic concepts, Objectives of QSAR, QSAR design and exp
erimentation, QSAR
descriptors and types, CoMFA and CoMSIA.

SMILES (Simplified Molecular Input Line Entry Specification)

Role of computers in Chemical search.




Suggested Readings
:

1.

Molecular Modeling for Beginners by Allan Hinchkliffe.

2.

Combinatorial Libra
ry Methods and Protocols edited by Lisa B. English.

3.

Molecular Modeling : Basic Principles and applications by Gerd Folkers,
Wolfgang sippl, Didier Rognan, Hans Dieter(EDT) Holtje
-

Science
-
2003

4.

Gupta S.P. Quantum Biology, New Age, 1996.

5.

Essentials of Drug D
esigning by V. Kothekar, Dhruv Publications.





Paper
-
VI: Molecular Modeling

Max Marks: 80






Lectures to be delivered: 60

Time allowed: 3 Hours





Pass Marks: 35%


The Question Paper will consist of five sections A, B, C, D, and E. Section A, B, C
and

D will have two questions from the respective sections of the syllabus and carry
15 marks each. Section
-
E consist of 10 short answer type questions which will cover
the entire syllabus uniformly and will carry 20 marks in all


Section A


Concepts of Molec
ular Modeling, Coordinate System: Cartesian and Internal, Surfaces,
Potential Energy Surfaces, Molecular Graphics and Structure visualization, Applications
of Molecular Graphics in Molecular Modeling.


Section
-
B

Force Fields: Molecular mechanics and Quantu
m mechanics, Features of Molecular
mechanics force fields. Bond stretching, Angle bending, Torsion terms, and Non
-

bonded
interactions: Electrostatic interaction, Vander walls interactions, and Local and Global
energy minima.


Section C


Energy

minimizatio
n methods: Derivatives and Non derivatives methods, Applications of
energy minimization, Energy minimization by Systematic search.

Molecular Dynamics: Methods and simulations, Monte Carlo method, Difference
between Molecular dynamics and Monte Carlo method
.


Section D


Quantum
mechanical
methods: Schrödinger equation,
molecular orbital calculations,
Hartree Fock Method
, semi
-
empirical methods.


Suggested Readings
:

1.

Molecular Modeling for Beginners by Allan Hinchkliffe.

2.

Combinatorial Library Methods and Proto
cols edited by Lisa B. English.

3.

Molecular Modeling : Basic Principles and applications by Gerd Folkers,
Wolfgang sippl, Didier Rognan, Hans Dieter(EDT) Holtje
-

Science
-
2003

4.

Gupta S.P. Quantum Biology, New Age, 1996.

5.

Essentials of Drug Designing by V. Kothe
kar, Dhruv Publications.



Paper
-
VII: Computational Biology

Max Marks: 80






Lectures to be delivered: 60

Time allowed: 3 Hours





Pass Marks: 35%


The Question Paper will consist of five sections A, B, C, D, and E. Section A, B, C
and D will have two q
uestions from the respective sections of the syllabus and carry
15 marks each. Section
-
E consist of 10 short answer type questions which will cover
the entire syllabus uniformly and will carry 20 marks in all

Section
-
A



Computational methods for Gene Pred
iction
: Gene Prediction in Prokaryotes and
eukaryotes: content based, signal based, homology based and comparative based
methods. Detection of Open Reading frames, machine Learning and probabilistic
Method, Artificial neural network, hidden markov Model, G
ene prediction algorithm.


Section
-
B


Promoter and Regulatory element prediction
: Promoter and regulatory elements in
prokaryotes, Promoter and Regulatory elements in eukaryotes, prediction algorithms: Ab
Initio algorithm, phylogenetic footprinting based m
ethods, expression profiling based
methods.

Transcription factor binding Sites, Splice site recognition methods, analysis of membrane
proteins
-
hydropathy plots, TransFac, PSORT, Pfam, Prosite, rVISTA, Gensplicer.


Section
-
C


Principle of X ray Crystallogr
aphy, NMR, Methods of single X ray diffraction of
macromolecule
-
Molecular replacement Method and multiple isomorphous replacement
method and direct method, fibre Diffraction.

Methods for prediction of secondary structure of proteins
: Ab initio based method
s
and homology based methods.

Methods for prediction of tertiary structure of proteins
: homology modeling,
threading, fold recognition, Ab initio based methods.

Secondary Structure analysis of RNA
: Types of RNA structure, RNA fold algorithm,
MFOLD, SFOLD,
Vienna RNA Package. RNA secondary structure prediction method:
ab initio, dot matrix, dynamic programming.


Section
-
D


Molecular interactions of Protein
-
Protein: Protein DNA, Protein carbohydrates, protein
ligand,Protein protein Interaction databases:

BIND
,DIP,GRID,STRING,KEGG,MetaCyc,EcoCyc.

Prediction algorithm for pathways and interaction
: Gene Neighbourhood,
Phylogenetic Profile, Gene Fusion, in silico two hybrids.



Suggested Readings:



1.

Setubal Joao and Meidanis Joao.Introduction to computational mol
ecular
Biology,PWS Publishing Company(An International Thomsaon Publishing
Company),(1997)Indian low priced edition

2.

Bioinformatics: sequence and Genome Analysi
s
,

by David Mount,

second
Edition.Cold Spring harbour
l
abortory press(2004)

3.

Discovering Genomics,
Proteomics and bioinformatics,2/E by A.Malcolm
Campbell and Laurie J.Heyer,Publisher:Benjamin Cummings(2007)





Paper
-
VIII: Immunotechnology and Biochemical Techniques

Max Marks: 80






Lectures to be delivered: 60

Time allowed: 3 Hours





Pass Marks: 3
5%


The Question Paper will consist of five sections A, B, C, D, and E. Section A, B, C
and D will have two questions from the respective sections of the syllabus and carry
15 marks each. Section
-
E consist of 10 short answer type questions which will cover

the entire syllabus uniformly and will carry 20 marks in all


Section A

Immune System: Humoral immunity


Introduction, Lymphocytes: Their origin and differentiation, Types of immune responses
B
-

Lymphocytes and their activation, structure and function of
immunologic,
immunologic classes and subclasses, generation of antibody diversity, Major
Histocompatibility Complex.


Section B

Immune system: Cellular immunity


Thymus derived lymphocytes( T cells) and their classification, Antigen presenting
cells(APC),
Macrophages, Langerhans cells their origin and function, mechanism of
phagocytosis, Identification of cell type of immune system, immunosuperresion,
immmuno tolerance.


Section C


Immunotechniques: Antiserum production, immunofluorescences, ELISA,
immunobl
otting, monoclonal antibodies, Fluoroscence assisted cell sorting(
Flowcytometry).

Chromatography: Definition, Principle and types: Paper, thin
-
layer, Adsorption, Ion
-
Exchange, Affinity, Gel
-
filteration, Gas, HPLC and FPLC.


Section D

Biochemical Methods o
f Analysis

Electrophoresis: Principles, types, moving paper Starch gel agar gel,
immunoelectrophoresis

Colorimertry, Flourier and Spectrometry: Principle of Beer and Lambert’s law: Principle,
description and application.

Principle of NMR, ESR, Mass spectr
ometer and X
-
ray diffraction, Fourier Transform:
Fourier Transform of discretely sampled dat
a, Fast Fourier Transform (FFT)


Recommended Books:

1.

I. Roitt, Essential Immunology, Blackwell Scientific Publications, Oxford(1991).

2.

E. Benjamin and S. Leskwitz, Im
munology: Ashort course, Wiley Liss NY(1991)

3.

Kuby, Immunology, Fourth edition.





Practical Paper
-
III

Pertaining to Theory P
aper
-
V & VI


10
0 marks


Chemoinformatics and Drug Designing


1.

To explore DrugBank.

2.

To explore PubChem.

3.

To study molecular representa
tion using SMILES.

4.

Perform Chemsketch.

5.

To design combinatorial library by using Smile software.

6.

Draw the structure using Chimera.

7.

To find active site of Protein using various software.

8.

To study bioavailability using Mol inspiration.

9.

Docking using HEX.

10.

Dock
ing using AUTODOCK.


Molecular Modeling


1.

RASMOL

2.

Cn3D

3.

CHIMERA

4.

SWISSPDBviewer

5.

CPH 2.0

6.

MODELLER

7.

SAVES




Practical Paper
-
IV

Pertaining to Theory P
aper
-
VII & VIII


10
0 marks


Computational Biology


1.

To find ORF using ORF finder

2.

Predict gene using Glimmer.

3.

To pr
edict exon and introns using GenScan.

4.

To Find Transcription factor binding sites using TransFac.

5.

Predict localization of proteins by PSORT.

6.

To perform search in Prosite

7.

To find protein family using Pfam.

8.

To find Transmembrane regions using Hydropathy plots

9.

To perform rVISTA

10.

Seconadry structure prediction by GOR and PORTER



Immunotechnology and Biochemical Techniques


1.

Immunodiffusion

2.

Immunoprecipitation

3.

Gel Electrophoresis

4.

Spectrophotometry

5.

UV Spectra

6.

TLC and other chromatographic Techniques

7.

ELISA





















Semester
-
III


Paper
-
IX: Programming in C++

and PERL

Max Marks: 80






Lectures to be delivered: 60

Time allowed: 3 Hours





Pass Marks: 35%


The Question Paper will consist of five sections A, B, C, D, and E. Section A, B, C
and D will have tw
o questions from the respective sections of the syllabus and carry
15 marks each. Section
-
E consists of 10 short answer type questions which will cover
the entire syllabus uniformly and will carry 15 marks in all.




Section
-
A

Methodologies:

C
oncept of str
uctural and object oriented programming advances in oops
methodologies.

Introduction to object oriented programming, characteristics of oops languages, c++
programming, basic operators, loops, arrays, pointer, principle of object oriented
programming.



Se
ction
-
B

Introduction of abstraction ,encapsulation ,inline function ,reference variables ,access
specifier ,information hiding ,friend functions ,friend classes, operator overloading
,inheritance ,extending classes ,types of inheritance ,virtual base class

,problems with
multiple inheritance, containership.



Section
-
C

Advanced pointers, pointers to classes, arrays, polymorphism, compile


Time and run time, virtual function abstract classes, pure virtual functions.

Files and stream building class libraries

in c++, file handling in c++, separate compilation
and name spaces ,template class and function ,exception handling .


Section
-
D


PERL programming
: An Introduction, Perl features, Operators, Statements, Loops,
Arrays, Arrays slices,

Hashes, List Processin
g, File Handles, Pattern Matching.


Suggested Readings
:

1.

Object oriented programming in C++ by Robert Laffore.

2.

Object oriented p
rogramming in C++ by S
troustrup,

Addision Wessely,2001.

3.

Object oriented programming in C++ by Balaguruswamy.

4.

Programming Perl by
O
Reilly
.

5.

Mastering Perl for Bioinformatics by James Tisdall.

6.

Object

Orriented in C++ by black book.

Paper
-
X : Advanced Computer Programming

Max Marks: 80






Lectures to be delivered: 60

Time allowed: 3 Hours





Pass Marks: 35%


The Question Paper will
consist of five sections A, B, C, D, and E. Section A, B, C
and D will have two questions from the respective sections of the syllabus and carry
15 marks each. Section
-
E consist of 10 short answer type questions which will cover
the entire syllabus uniform
ly and will carry 20 marks in all



SECTION A


Introduction to HTML, Structure of HTML Pages, Text formatting Tags, adding graphics
with image tag, Image element attributes, using image as links, creating internal and
external links. Tables: Presenting inf
ormation in tables, frameset, table as lay out tools,
nested tools. Frames: using frames, frameset, target links, no frame element.

Forms: using HTML forms, input control elements and attributes, processing forms.


SECTION B


Basic of active server pages,
introduction of ASP Objects, writing server
-
side code using
components, accessing database with ASP and ADO, ASP, Application advanced ASP,
beyond asp.


SECTION C


XML
-

Introduction, anatomy of XML document, using xml markup, working with
elements and att
ributes, checking well formedness. X
ML

objects exploiting entities,
checking validity creating xml links, viewing xml in internet explorer, viewing xml in
other browsers, even
-
driven programming styling xml with CSS.


SECTION
D


Introduction to application

development using Visual Basic. Variables, standard controls,
working with code and forms. Data access using data control.



Suggested readings:


1.

Active Server pages teach yourself in 21 days.

2.

XML for Bioinformatics by Ethan Cerami.

3.

XML teach yourself in
21 days, published by SAMS Techmedia.

4.

Visual Basic published by Schaum’s Outline.

5.

Mastering in Visual Basic 6.0 Published by BPB.



Paper
-
XI: Genomics and Proteomics

Max Marks: 80






Lectures to be delivered: 60

Time allowed: 3 Hours





Pass Marks: 35%


The Question Paper will consist of five sections A, B, C, D, and E. Section A, B, C
and D will have two questions from the respective sections of the syllabus and carry
15 marks each. Section
-
E consist of 10 short answer type questions which will cover
t
he entire syllabus uniformly and will carry 20 marks in all


Section
-
A

Organization and Structure of Genomes
: Genome Size, Sequence Complexity
-
Intron
and Exons, repetitive Content of eukaryotic genome.DNA sequencing: Maxam Gilbert
Method, Sanger’s Method,
Automated DNA sequencing. Genome Sequencing Strategies:
Hierachical (Clone contig) and shotgun method.


Section
-
B

Genome Sequencing
: Genetic, Physical, cytological.

Polymorphism, molecular markers
-

RFLP, VNTR, AFLP, SSR, RAPD.

SNP, SNP detection methods
-
S
SCP, PCR based, DGGE, TGGE, SNP diseases, SNP
databases
-
dbSNP, Pharmacogenomics, Pharmacotherapeutics.Use of SNP information in
pharmacogenomics and personalized medicine.


Section
-
C

Introduction to proteomics, Analysis of proteome
-
2D PAGE: Sample preparat
ion,
solubalization, reduction, resolution, reproducibility (overview only)

Mass Spectrometry based methods for protein identification: De novo sequencing using
Mass spectrometric data, use of MALDI TOF and related methods for protein mass
determination.

D
etermination of Protein structure: Edman
n

Degradation


Section
-
D

Protein
: Determination of sizes (Sedimentation analysis, gel filtration, SDS PAGE,
Native PAGE).

Post Translational modification: Methylation, Glycosylation, lipid attachment and
disulphide b
ond formation.

Protein Protein Interaction: FRET, Yeast Two Hybrid, co
-
immunoprecipitation


Suggested Readings:

1

Setubal Joao and Meidanis Joao.Introduction to computational molecular Biology,
PWS Publishing Company (An International Thomson Publishing Com
pany),
(1997) Indian low priced Edition harbour Laboratory Press (2004).

2

Bioinformatics: sequence and Genome Analysis by David Mount, second Edition.
Cold Spring

3

Discovering Genomics, Proteomics and Bioinformatics,2/E by A. Malcolm
Campbell and Laurie J.
Heyer, Publisher :Benjamin Cummings(2007)


Paper
-
XII: Functional Genomics

Max Marks: 80






Lectures to be delivered: 60

Time allowed: 3 Hours





Pass Marks: 35%


The Question Paper will consist of five sections A, B, C, D, and E. Section A, B, C
and D
will have two questions from the respective sections of the syllabus and carry
15 marks each. Section
-
E consist of 10 short answer type questions which will cover
the entire syllabus uniformly and will carry 20 marks in all

Section A


Introduction to Micro

array, Types of Micro array: DNA & Protein, cDNA micro array
technology, Oligonucleotide microarray technology, Microarray experimentation, And
and Microarray data analysis: Image processing, normalizing expression measurement,
Descriptive and inferential

statistical methods, Cluster analysis, Applications of
Microarray, Microarray databases: SMD, GEO, YMD.


Section B


Introduction to ESTs, ESTs clustering assembly and EST databases, Alternative splicing,

Differential display, Regulatory RNA: SnRNA, microR
NA, SiRNA, RNAi, antisense
RNA technology, Secondary structure analysis of RNA: Stem and Loop structure,


Section C


Comparative Genomics: Homologous: Orthologous and Paralogous, Analogous,
Xenologous, Horozontal gene transfer.

Orthologous identification
BLAST and Reciprocal Best Hit, Cluster of Orthologous
Groups, Synteny, Gene Order, Phylogenetic footprinting, Use of comparative genomics
in gene annotation and function prediction.





Section D


Web based servers and softwares for gemone analysis: Ensem
bl, UCSC and NCBI
genome browsers, Large genome alignments: Problems of complexity, reapeats and size.

Whole Genome Browsers: MUMmer, BLASTZ, LAGAN, AVID, VISTA and PipMaker.


Recommended Books:


1.

Bioinformatics: Sequence and Genome Analysis, by David Mount
, Second
edition, Cold Spring Harbor Laboratory Press(2004)

2.

Discovering Genomics, Proteomics and Bioinformatics, 2/E by A. Malcolm
Campbell and Laurei J. Heyer, publisher: Benjamin cimmings(2005)

3.

Proteins: Structures and Molecular Properties by T.E. Creigh
ton.W.H.Freeman &
Company 2
nd

Edition, 1993.

4.

Microarray
Bioinformatics

by Dov Stekel, Published by Cambridge University
Press, 1
st

Edition, 2003.





Practical Paper
-
V

Pertaining to Theory P
aper
-
VIII & IX


10
0 marks


Programming in C++


1.

WAP to calculate ad
dition,

subtraction,

multiplication and division.

2.

WAP to calculate greatest number out of three.

3.

WAP to using switch statement.

4.

WAP to using while,

do while and for loop.

5.

WAP to using function overloading.

6.

WAP to using Function Parameter techniques.

7.

WAP to

using operator overloading.

8.

WAP to using structures.

9.

WAP to using Class and objects.

10.

WAP to constructor.

11.

WAP to using inheritance.

12.

WAP to using virtual functions.

13.

WAP to using Virtual base classes.

14.

WAP to using template classes.

15.

WAP to using Exception Han
dling.

16.

Writing codes in PERL



Advanced Computer Programming


1)

Make a web page by using text format tags.

2)

Make a web page by using different types of ordered lists.

3)

Make a web page by using different types of unorder
ed lists.

4)

Make a web page by using definition list.

5)

Make a web page by using table (with all table attributes)

6)

Make a web page by using images.

7)

Make a web page to accept data from user using forms.

8)

Make a web page by using absolute hyperlink.

9)

Make a web
page by using relative hyperlink.

10) Make a web page in ASP by using Built
-
in
-
functions.

11) Make a web page in ASP by using Class and objects.

12) Make a web page in ASP which accepts data form user and send it by using post


or Get method.

1
3)

Make an advertisement page using AD
rotator

in ASP.

14) Make a web page in ASP to accept login name and password from user and

display welcome page using ADO.

15
) Writing codes with XML.

16
) Writing codes with XML attributes and elements.

17
)

Writing co
des using internal DTD.

18
) Writing codes using entities with DTD.

19
)

Writing codes using CSS with XML document.

20) W.A.P in V.B to demonstrate the use of textbox, label, button control.

21) W.A.P in V.B to demonstrate the use of listbox and dropdownlist
.

22)

W.A.P in V.B to demonstrate the use of checkbox and radio button.

23)

W.A.P in V.B using scrollbars and image control.

24) W.A.P in V.B to demonstrate the use of Data access using data control



Practical Paper
-
VI

Pertaining to Theory P
aper
-
XI & XII


10
0 marks

Genomics and Proteomics


1.

NCBI Mapviewer

2.

dbSNP

3.

Swiss 2D PAGE

4.

STRING

5.

BIND

6.

DIP

7.

KEGG

8.

BRENDA

9.

E
-
PCR

10.

SDS PAGE





Functional Genomics


1.

To analyze and Normalize Microarray data in Stanford Microarray Database.

2.

COG Database

3.

SCOP

4.

CATH

5.

mFOLD

6.

NCBI Genome Br
owser

7.

Ensembl

8.

UCSC Browser

9.

VISTA package








Semester
-
IV


Paper
-

XIII
Java Programming & Data Mining

Max Marks: 80






Lectures to be delivered: 60

Time allowed: 3 Hours





Pass Marks: 35%


The Question Paper will consist of five sections A, B, C, D
, and E. Section A, B, C
and D will have two questions from the respective sections of the syllabus and carry
15 marks each. Section
-
E consist of 10 short answer type questions which will cover
the entire syllabus uniformly and will carry 20 marks in all


Section


A

Object Oriented Concept, Introduction to Class, Object, Abstraction, Encapsulation,
Polymorphism, Importance of Java, Data Types, Variables, arrays. Operators: Arithmetic,
Relational, Logical, Unary, Conditional Operators. Control Statements, C
reating Classes,
Declaring Objects, Methods, Access Specifiers. Constructor: Introduction to Constructor,
Method with Argument Passing, Method Overloading, Constructor Overloading.


Section


B

Inheritance: Inheritance Basics, Types of Inheritance, using S
uper to Call Super Class
Constructor, Interface Defining, Implementing Interface, Abstract Classes Final with
Inheritance, Final to Prevent Overloading. Exception Handling: Using Try & Catch,
Multiple Catch Classes, throw, final, Built own Exception.


Se
ction
-

C

I/O Applets: Applet Basics, Applet Classes, Applet Life Cycle, Calling Applet with
Parameters, Difference b/w application and Applet, Applet Paint, Repaint, draw line,
Rectangle, Oval, String using Applet, Stream: Stream Basics, Byte Streams, Cha
racter
Streams, Reading Congeal Input, Interface with AWT.


Section


D

Data Mining: Data Mining Basics, Knowledge Discovery in Databases, Architecture of
Determining, Decision Tree, Transactional Database, Data Warehouse Database.
Introductory Data Secu
rity Concept. Discretionary and Mandatory Access Controls,
Secure Architecture, Secure Transactional processing.



Recommended books:

1.

JAVA 2: The Complete Reference by Patrick Naughton, Herbert Schidt,
Osbourne Publishing; 3
rd

Edition.

2.

Teach Yourself

JAVA in 21 Days Publisher: Sams net BK & CD ROM edition.

3.

Data Minig Techniques by Arun K. Pujari, Publisher: University (India) Press
Private Limited.

4.

Data Mining Concepts & Techniques by Jaiwei Han and Micheline Kamber,
Publisher: Elsevier, 2
nd

Edition
.




Paper
-
XIV : Numerical Methods and Optimization Techniques


Max Marks:
80






Lectures to be delivered: 60

Time allowed: 3 Hours





Pass Marks: 35%


The Question Paper will consist of five sections A, B, C, D, and E. Section A, B, C
and D will have

two questions from the respective sections of the syllabus and carry
15 marks each. Section
-
E consist of 10 short answer type questions which will cover
the entire syllabus uniformly and will carry 20 marks in all




Section


A


Numerical Methods & Optimization. Errors involved in the construction of a

mathematical model of the real physical process. Errors in the numerical

approximation of the mathematical model (truncation errors).
Errors in the actual

computation using a computer (round off errors )



Section


B


Minimization or Maximization of Functions: (Problems with minimum number of

Iterations). Golden section search in on
e dimension, parabolic interpolation.




Section


C


Brent’s method in one dimension, one dimensional search with first derivatives.

Downhill simplex method in multi dimensions, directions set (powell’s
) methods

in multi dimensions.



Section


D


Integration of ordinary Differential Equations: Runge
-
Kutta Method, taylor’s

series Method, Euler’s Method, Lagrange’s multiplier method, Modified Midpoint
Me
thod.



Suggested readings:


1.

Chopra, S.C. Raman and Canale, P. numerical methods for Engineers with
personal computer applications.

2.

Engineering Mathematics by T.Veerarajan, Tata Mc
-
Graw Hill Publishing
Company

3.

Optimization techniques by Singiresu S. Rao,

New age International (F)
Limited.

4.

Sastry, S.S. (1993).Introductory methods of numerical analysis. Prentice Hall of
IndiaPvt. Ltd. New Delhi.

5.

Venkataraman, M.K.(1999). International student Edition numerical methods in
science and engineering . Nationa
l publishing company, Chennai.





Practical Paper
-
VII

Pertaining to Theory P
aper
-
XIII & XIV


10
0 marks


Java Programming & Data Mining


1.

Writing Codes in JAVA.


Numerical Methods and Optimization Techniques

1.

Finding errors

2.

Rounding off error

3.

Maximiz
ing a function

4.

Minimizing a function

5.

Integrating a differential equation

6.

Approximation of function using Taylor’s series and Runge
-
Kutta method.






Project Work; in plant Training, Seminar and industrial Visit


Satisfactory/Unsatisfactory


Pr
oject Work shall be evaluated by two external examiners satisfactory or Unsatisfactory.
After the evaluation, two examiners will conduct Viva Voce examination. Seminar on
project will be evaluated by team of three teachers as Satisfactory/ Unsatisfactory.
The
awards of Seminar and industrial visits shall be communicated by the Head of the
Department/ Principal before the commencement of the exams.