department of botany kumaun university ssj campus almora brochure... · 1 department of botany...
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Department of Botany
KUMAUN UNIVERSITY
SSJ CAMPUS
ALMORA
Information brochure
(2014-20125)
Admission to M.Sc. Bioinformatics
&
PG diploma in Bioinformatics
Self-finance course
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WELLCOME !!!!!
Bioinformatics is a multi-disciplinary subject. It is important to the modern day
study of all area of biology and essential to 21st century biological research. Bio-
informatics includes the concepts of Molecular biology, Biochemistry, Statistics,
Physic, Mathematics, Computer science, and Information technology to carry out
research with aim of knowledge discovery and solving the challenging problems of
modern biological fields.
Area of Applications of Bioinformatics:
Drug discovery
Medical informatics
Molecular medicine
Personalized medicine
Preventative medicine
Gene therapy
Genome analysis
Computational tools and biological database development
Biotechnology
Forensic analysis
Evolutionary studies
Improve nutritional quality and
Crop improvement
Scope of bioinformatics:
Bioinformatics career is increasingly attracting the youngsters in India today. The
scope of bioinformatics is in areas like database design and maintenance, sequence
assembly, proteomics, drug design clinical pharmacologist, sequence analysis,
informatics developer and bio-analytics. Excellent job opportunities are available in
Biotech and Pharmaceutical companies in India and abroad. In India, companies like
Reliance Life Science, IBM Life Sciences Wipro, Satyam, TCS Accelrys, Silicon
Genetics and Tessella offer good employments to the bioinformatics candidates.
Research institutes of ICMR, DBT, CSIR and other research institutes regularly
require Bioinformatian as JRF, SRF, RA and scientist. Candidates can also get job
as Lecture/ Assistant Professor in government or private Universities and colleges.
The increasing demand of bioinformatics candidates, presents a good career in the
this fields.
Contact- Dr Subhash Chandra
Mob. 7351976362
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Eligibility:
Graduate students with 45% marks or equivalent CGPA in any background in
Science & Technology ( eg. Biology, Biotechnology, Math, Agriculture, MBBS,
Computer Science, IT, B.PHARM, B.TECH etc.
(Students in last semester or waiting for final result also can apply)
Admission will be on the basis of merit.
Reservation will be as per State Govt. rules.
Schedule of Admission:
Applications are invited for admission to first Semester M.Sc. Bioinformatics and
PG Diploma in Bioinformatics at Department of Botany, Kumaun University, SSJ
Campus, Almora.
S.No.
Particulars Date
1 Last Date for submission of
Forms
30 June 2014
2 Commencement of session August 2014
How to apply:
a) Information brochure and application form can be downloaded from website
www.kuntl.in.
b) Application must be sent on the prescribed format along with a demand draft of
Rs.500/- (Five hundred only), in favour of Assistant Account Officer
Bioinformatics course Department of Botany, payable at State bank of India,
Almora so as to reach the Department on or before 30 June, 2014. Forms can be
submitted with late fee of Rs. 250 till 15th
July.2014.
c) Documents required to be attached along with the application form: Self- attested
photocopies of certificate in support of educational qualification and category
certificate.
d)Application form completed in all respects should reach, The Co-ordinator,
Bioinformatics programme, Department of Botany, Kumaun University, SSJ
Campus, Almora- 263601, Uttarakhand by hand/ speed post/registered post on or
before 30 th June, 2014. The Department of Botany shall not be responsible for any
delay.
Details of Seats-There shall be 40 seats for M.Sc Bioinformatics and 60 Seats for
PG Diploma Bioinformatics. The seats may be increased or decreased at the
discretion of the University without any further notification.
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Fee Structure M.Sc. Bioinformatics (per Semester)
Remark: Examination fee per semester will be charged as per as University rules.
No Fee Description I Sem II Sem III Sem IV Sem 1 Tut ion Fee 25000 25000 25000 25000
2 Laboratory Fee 3500 3500 3500 3500
3 Library Fee 1500 1500 1500 1500
4 Sports Fee 300 300 300 300
5 Reading Room Fee 30 30 30 30
6 Development Fee 120 120 120 120
7 Inflation Fee 300 300 300 300
8 Department Exam
Fee 25 25 25 25
9 Student Union Fee 40 40 40 40
10 Campus Fee 20 20 20 20
11 Student Welfare Fee 20 20 20 20
12 Cultural Association
Fee 20 20 20 20
13 Medical Fee 20 20 20 20
14 Identity Card Fee 25 25 25 25
15 Insurance Fee 101 101 101 101 16 Practical/Viva
(per subject)
75 75 75 75
17 Admission Fee 50 50 50 50
18 Campus Magazine
Fee 40 40 40 40
19 Registration Fee 100 100 100 100 20 Enrollment Fee 50 NA NA NA 21 Caution Fee 2000 NA NA NA
Total(Rs.) 33336 31286 31286 31286
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Fee Structure for PG Diploma Bioinformatics (per Semester)
Remark: Examination fee per semester will be charged as per as University rules.
S.No Fee Description I Sem II Sem 1 Tut ion Fee 25000 25000
2 Laboratory Fee 3500 3500
3 Library Fee 1500 1500
4 Sports Fee 300 300
5 Reading Room Fee 30 30
6 Development Fee 120 120
7 Inflation Fee 300 300
8 Department Exam
Fee 25 25
9 Student Union Fee 40 40
10 Campus Fee 20 20
11 Student Welfare Fee 20 20
12 Cultural Association
Fee 20 20
13 Medical Fee 20 20
14 Identity Card Fee 25 25
15 Insurance Fee 101 101 16 Practical/Viva
(per subject)
75 75
17 Admission Fee 50 50
18 Campus Magazine
Fee 40 40
19 Registration Fee 100 100 20 Enrollment Fee 50 NA 21 Caution Fee 2000 NA
Total (Rs.) 33336 1286 31286
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Kumaun University, SSJ Campus, Almora
Semester I
Course code Title
BIF 1 Basic Mathematics
BIF 2 Computer Fundamentals and
Biostatistics
BIF 3 Biomolecules
BIF 4 Cell and Developmental Biology
BIF 5 Practicals
Comprehensive Viva Voce
Total Marks
Semester II
Course code Title
BIF6 Bioinformatics I
BIF7 Object Oriented Programming
through ‘C++’
BIF 8 Molecular Biology
BIF 9 Design and Analysis of algorithms
BIF 10 Internet and Web Based
Programming (CGI PERL &
HTML)
BIF 11 Practicals
Seminars
Comprehensive Viva Voce
Total Marks
Semester III
Course code Title
BIF 12 Bioinformatics II
BIF 13 Bioinformatics III
BIF 14 Database management System
BIF 15 Recombinant DNA Technology
BIF 16 Java Programming
BIF 17 Assignments/ Practical
Comprehensive Viva Voce
Seminars
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Semester IV
Course code Title
BIF 18 Project Work
Comprehensive Viva Voce
Seminars
BASIC MATHEMATICS
M.Sc. Bioinformatics Semester I
UNIT 1- Set theory : Introduction, Examples of Sets, Representation of a set (Roaster form
and Setbuilder form), Notation, Different types of sets- null set, singleton set, finite set,
infinite set, sub set, proper and improper subsets, equal sets, equivalent sets, universal set,
disjoint set, Set operations- Union, properties of union of sets, Intersection of sets, properties
of insertion operation, De Morgan’s Law, Complement of a set, Set Difference, Venn
diagram, problem based on sets. UNIT 2- Limits: Constants, Types of constants, Variables, Types of Variables, Function,
Types of function,Right hand and left hand limits, Working rule for finding out the limit,
problems based on limits. Continuity: Define; point out discontinuity, Method of finding the continuity, Continuity
fromright and from left, Problem based on continuity. Differentiability: Basic concept of the derivatives of function, Definition of the derivative
offunction, right hand and left hand derivatives, Condition for differentiability of a function,
Problem based on differentiability. UNIT 3-The binomial theorem: Define, Binomial theorem for a positive integral index,
BinomialExpansion, Finding middle term, general term, Binomial theorem for any index. UNIT 4-Probability: Introduction, Events and types of events, Probability of events,
Mutually exclusiveevents, favorable events, exhaustive events, independent events, addition
theorem on probability, conditional probability, Multiplication theorem, Problem based on
probability theorem, Baye’s theorem, Problem based on Baye’s theorem. UNIT 5-Differentiation and Integration: Introduction, Basic concepts and problems related
to differentiationand integration.
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COMPUTER FUNDAMENTALS AND BIOSTATISTICS
M.Sc. Bioinformatics Semester I
Unit I- Fundamental concepts in applied probability; Exploratory data analysis and statistical
inference; Probability and analysis of one and two way samples; discrete and continuous
probability models; Expectation and variance; Central limit theorem; Inference; Hypothesis;
Critical region and error probabilities; Tests for proportion; Equality of proportions; equality of
means of normal populations(variance known, variance unknown); Chi-square test for
independence; P-value of the statistic; Confidence limits; Introduction to one way and two-way
analysis of variance; Data transformations Unit II-Elements of programming languages - C and PERL; Data base concept; Database
management system; Database browsing and Data retrieval; Sequence database and genome
database; Data Structures and Databases; Databases such as GenBank; EMBL; DDBJ;
Swissprot; PIR; MIPS; TIGR; Hovergen; TAIR; PlasmoDB; ECDC; Searching for sequence
database like FASTA and BLAST algorithm. Unit III-Cluster analysis; Phylogenetic clustering by simple matching coefficients; Sequence
Comparison; Sequence pattern; Regular expression based pattern; Theory of profiles and their
use in sequence analysis; Markov models; Concept of HMMS; Baum-Welch algorithm; Use of
profile HMM for protein family classification; Pattern recognition methods Unit IV-Goals of a Microarray experiment; Normalization of Miroarray data; Detecting
differential gene expression; Principal component analysis; Clustering of microarray data;
Structure determination by X-ray crystallography; NMR spectroscopy; PDB (Protein Data Bank)
and NDB (Nucleic Acid Data Bank); File formats for storage and dissemination of molecular
structure. Unit V-Methods for modeling; Homology modeling; Threading and protein structure prediction;
Structure-structure comparison of macromolecules with reference to proteins; Force fields;
Molecular energy minimization; Monte Carlo and molecular dynamics simulation Practicals-Introduction to MS EXCEL-Use of worksheet to enter data, edit data, copy data,
move data. Use of in-built statistical functions for computations of Mean, S.D., Correlation,
regression coefficients etc. Use of bar diagram, histogram, scatter plots, etc. graphical tools in
EXCEL for presentation of data. Introduction to SYSTAT package. Searching PubMed ,
Introduction to NCBI, NCBI data bases, BLAST BLASTn, BLASTp, PSI-BLAST, Sequence
manipulation Suite, Multiple sequence alignment, Primer designing, Phylogenetic Analysis.
Protein Modeling, Protein structure Analysis, Docking, Ligplot interactions.
BIOMOLECULES
M.Sc. Bioinformatics Semester I
Unit - I Chemical basis of life; Composition of living matter; Water – properties, pH, ionization and
hydrophobicity; Emergent properties of biomolecules in water; Biomolecular hierarchy;
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Macromolecules; Molecular assemblies; Structure-function relationships Amino acids – structure
and functional group properties; Peptides and covalent structure of proteins; Elucidation of
primary and higher order structures; Evolution of protein structure; Structure-function
relationships in model proteins like ribonuclease A, myoglobin, hemoglobin, chymotrypsin etc.;
Tools to characterize expressed proteins.
Unit - II Enzyme catalysis – general principles of catalysis; Quantitation of enzyme activity and
efficiency; Enzyme characterization and Michaelis-Menten kinetics; Relevance of enzymes in
metabolic regulation, activation, inhibition and covalent modification; Single substrate enzymes
Unit - III Sugars - mono, di, and polysaccharides; Suitability in the context of their different functions-
cellular structure, energy storage, signaling; Glycosylation of other biomolecules - glycoproteins
and glycolipids; Lipids - structure and properties of important members of storage and
membrane lipids; lipoproteins
Unit - IV Biomembrane organization - sidedness and function; Membrane bound proteins - structure,
properties and function; Transport phenomena, Nucleosides, nucleotides, nucleic acids -
structure, diversity and function; sequencing; Brief overview of central dogma
Unit - V Bioenergetics-basic principles; Equilibria and concept of free energy; Coupled processes;
Glycolytic pathway; Kreb’s cycle; Oxidative phosphorylation; Photosynthesis; Elucidation of
metabolic pathways; Logic and integration of central metabolism; entry/ exit of various
biomolecules from central pathways; Principles of metabolic regulation; Regulatory steps;
Signals and second messengers.
CELL BIOLOGY AND GENETICS
M.Sc. Bioinformatics Semester I
Unit I-Cell Theory & Methods of Study;Microscope and its modifications – Light, phase
contrast and interference, Fluorescence, Confocal, Electron (TEM and SEM), Electron tunneling
and Atomic Force Microscopy, etc.
Membrane Structure and Function;Structural models; Composition and dynamics; Transport
of ions and macromolecules; Pumps, carriers and channels; Endo- and Exocytosis; Membrane
carbohydrates and their significance in cellular recognition; Cellular junctions and adhesions;
Structure and functional significance of plasmodesmata.
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Unit II-Organelles;Nucleus – Structure and function of nuclear envelope, lamina and nucleolus;
Macromolecular trafficking; Chromatin organization and packaging; Cell cycle and control
mechanisms; Mitochondria – structure, organization of respiratory chain complexes, ATP
synthase, Structure-function relationship; Mitochondrial DNA and male sterility; Origin and
evolution; Chloroplast– Structure-function relationship; Chloroplast DNA and its significance;
Chloroplast biogenesis; Origin and evolution.
Unit III-Endo-membrane System and Cellular Motility;Structure and function of
microbodies, Golgi apparatus, Lysosomes and Endoplasmic Reticulum; Organization and role of
microtubules and microfilaments; Cell shape and motility; Actin-binding proteins and their
significance; Muscle organization and function; Molecular motors; Intermediate filaments;
Extracellular matrix in plants and animals.
Unit IV-Cellular Movements and Pattern Formation;Laying of body axis planes;
Differentiation of germ layers; Cellular polarity; Model plants like Fucus and Volvox; Maternal
gene effects; Zygotic gene effects; Homeotic gene effects in Drosophila; Embryogenesis and
early pattern formation in plants; Cell lineages and developmental control genes in
Caenorhabditis.
Unit V-Differentiation of Specialized Cells; Stem cell differentiation; Blood cell formation;
Fibroblasts and their differentiation; Cellular basis of immunity; Differentiation of cancerous
cells and role of proto-oncogenes; Phase changes in Salmonella; Mating cell types in yeast;
Surface antigen changes in Trypanosomes; Heterocyst differentiation in Anabaena; Sex
determination in Drosophila. Plant Meristem Organization and Differentiation; Organization of Shoot Apical
Meristem(SAM); Organization of Root Apical Meristem(RAM); Pollen germination and pollen
tube guidance; Phloem differentiation; Self-incompatibility and its genetic control; Embryo and
endosperm development; Heterosis and apomixis.
BIOINFORMATICS-I
M.Sc. Bioinformatics Semester II
UNIT 1- Introduction and Bioinformatics Resources: Knowledge of various databases and
bioinformatics tools available at these resources, the major content of the databases, Literature
databases:
• Nucleic acid sequence databases: GenBank, EMBL, DDBJ • Protein sequence databases: SWISS-PROT, TrEMBL, PIR, PDB • Genome Databases at NCBI, EBI, TIGR, SANGER
• Other Databases of Patterns/Motifs/System Biology (Gene and protein network database and
resources) UNIT 2-Sequence analysis: • Various file formats for bio-molecular sequences: genbank, fasta, gcg, msf, nbrf-pir etc. • Basic concepts of sequence similarity, identity and homology, definitions of homologues,
orthologues, paralogues. • Scoring matrices: basic concept of a scoring matrix, PAM and BLOSUM series.
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• Sequence-based Database Searches: what are sequence-based database searches, BLAST and
FASTA algorithms, various versions of basic BLAST and FASTA. UNIT 3- Pairwise and Multiple sequence alignments: basic concepts of sequence alignment,
Needleman &Wuncsh, Smith & Waterman algorithms for pairwise alignments, Progressive and
hierarchical algorithms for MSA. Use of pairwise alignments and Multiple sequence alignment
for analysis of Nucleic acid and protein sequences and interpretation of results. UNIT 4-Phylogeny: Phylogenetic analysis, Definition and description of phylogenetic trees and
various types of trees, Method of construction of Phylogenetic trees [distance based method
(UPGMA, NJ), Maximum Parsimony and Maximum Likelihood method] UNIT 5-Current Advancements in Bioinformatics: Introduction to System Biology, Structural
Biology, Structural bioinformatics, Chemoinformatics, Immunoinformatics etc.
OBJECT ORIENTED PROGRAMMING THROUGH 'C++'
M.Sc. Bioinformatics SemesterII
UNIT-I-Overview of C++ : Object oriented programming, Introducing C++ classes, Concepts of
object oriented programming. Classes & Objects : Classes, Structure & classes, Union &
Classes, Friend function, Friend classes, Inline function, Scope resolution operator, Static class
members: Static data member, Static member function, Passing objects to function, Returning
objects, Object assignment. UNIT-II-Array, Pointers references & The Dynamic Allocation operators : Array of objects,
Pointers to object, Type checking C++ pointers, The This pointer, Pointer to derived types,
Pointer to class members, References: Reference parameter, Passing references to objects,
Returning reference, Independent reference, C++ ’s dynamic allocation operators, Initializing
allocated memory, Allocating Array, Allocating objects.Constructor & Destructor : Introduction,
Constructor, Parameterized constructor, Multiple constructor in a class, Constructor with default
argument, Copy constructor, Default Argument, Constructing two dimensional Array,
Destructor. UNIT-III-Function & operator overloading : Function overloading, Overloading constructor
function finding the address of an overloaded function, Operator Overloading: Creating a
member operator function, Creating Prefix & Postfix forms of the increment & decrement
operation, Overloading the shorthand operation (i.e. +=,-= etc), Operator overloading
restrictions, Operator overloading using friend function, Overloading New & Delete,
Overloading some special operators, Overloading [ ], ( ), -, comma operator, Overloading << . UNIT-IV- Inheritance : Base class Access control, Inheritance & protected members, Protected
base class inheritance, Inheriting multiple base classes, Constructors, destructors & Inheritance,
When constructor & destructor function are executed, Passing parameters to base class
constructors, Granting access, Virtual base classes . Virtual functions &Polymorphism : Virtual
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function, Pure Virtual functions, Early Vs. late binding UNIT-V-Creating string objects, manipulating string objects, relational operators, string
characteristics, comparing and swapping
MOLECULAR BIOLOGY
M.Sc. Bioinformatics Semester II
Unit I-Genome organization;Organization of bacterial genome; Structure of eukaryotic
chromosomes; Role of nuclear matrix in chromosome organization and function; Matrix binding
proteins; Heterochromatin and Euchromatin; DNA reassociation kinetics (Cot curve analysis);
Repetitive and unique sequences; Satellite DNA; DNA melting and buoyant density;
Nucleosome phasing; DNase I hypersensitive regions; DNA methylation & Imprinting. Unit II-DNA Structure; Replication; Repair & Recombination;Structure of DNA - A-,B-, Z-
and triplex DNA; Measurement of properties-Spectrophotometric, CD, AFM and Electron
microscope analysis of DNA structure; Replication initiation, elongation and termination in
prokaryotes and eukaryotes; Enzymes and accessory proteins; Fidelity; Replication of single
stranded circular DNA; Gene stability and DNA repair- enzymes; Photoreactivation; Nucleotide
excision repair; Mismatch correction; SOS repair; Recombination: Homologous and non-
homologous; Site specific recombination; Chi sequences in prokaryotes; Gene targeting; Gene
disruption; FLP/FRT and Cre/Lox recombination. Unit III-Prokaryotic & Eukaryotic Transcription;Prokaryotic Transcription; Transcription
unit; Promoters- Constitutive and Inducible; Operators; Regulatory elements; Initiation;
Attenuation; Termination-Rho-dependent and independent; Anti-termination; Transcriptional
regulation-Positive and negative; Operon concept-lac, trp, ara, his, and gal operons;
Transcriptional control in lambda phage; Transcript processing; Processing of tRNA and rRNA
Eukaryotic transcription and regulation; RNA polymerase structure and assembly; RNA
polymerase I, II, III; Eukaryotic promoters and enhancers; General Transcription factors; TATA
binding proteins (TBP) and TBP associated factors (TAF); Activators and repressors;
Transcriptional and post-transcriptional gene silencing Unit IV-Post Transcriptional Modifications; Processing of hnRNA, tRNA, rRNA; 5'-Cap
formation; 3'-end processing and polyadenylation; Splicing; RNA editing; Nuclear export of
mRNA; mRNA stability; Catalytic RNA. Translation & Transport; Translation machinery; Ribosomes; Composition and assembly;
Universal genetic code; Degeneracy of codons; Termination codons; IsoacceptingtRNA; Wobble
hypothesis; Mechanism of initiation, elongation and termination; Co- and post-translational
modifications; Genetic code in mitochondria; Transport of proteins and molecular chaperones;
Protein stability; Protein turnover and degradation Unit V-Mutations; Oncogenes and Tumor suppressor genes;Nonsense, missense and point
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mutations; Intragenic and Intergenic suppression; Frameshift mutations; Physical, chemical and
biological mutagens; Transposition - Transposable genetic elements in prokaryotes and
eukaryotes; Mechanisms of transposition; Role of transposons in mutation; Viral and cellular
oncogenes; Tumor suppressor genes from humans; Structure, function and mechanism of action
of pRB and p53 tumor suppressor proteins; Activation of oncogenes and dominant negative
effect; Suppression of tumor suppressor genes; Oncogenes as transcriptional activators.
DESIGN & ANALYSIS OF ALGORITHM
M.Sc. Bioinformatics Semester II
UNIT I-Basic Concepts of Algorithms; Introduction – Notion of Algorithm – Fundamentals of
Algorithmic Solving – Important Problem types –Fundamentals of the Analysis Framework –
Asymptotic Notations and Basic Efficiency Classes. UNIT II-Mathematical Aspects and Analysis of Algorithms; Mathematical Analysis of Non-
recursive Algorithm – Mathematical Analysis of Recursive Algorithm –Example: Fibonacci
Numbers – Empirical Analysis of Algorithms – Algorithm Visualization. UNIT III-Analysis of Sorting and Searching Algorithms;Brute Force – Selection Sort and
Bubble Sort – Sequential Search and Brute-force string matching – Divide and conquer – Merge
sort – Quick Sort – Binary Search – Binary tree-Traversal and Related Properties – Decrease and
Conquer – Insertion Sort – Depth first Search and Breadth First Search. UNIT IV-Algorithmic Techniques;Transform and conquer – Presorting – Balanced Search
trees – AVL Trees – Heaps and Heap sort – Dynamic Programming – Warshall’s and Floyd’s
Algorithm – Optimal Binary Search trees – Greedy Techniques – Prim’s Algorithm – Kruskal’s
Algorithm – Dijkstra’s Algorithm – Huffman trees. UNIT V-Algorithm Design Methods;Backtracking – n-Queen’s Problem – Hamiltonian Circuit
problem – Subset-Sum problem – Branch and bound– Assignment problem – Knapsack problem
– Traveling salesman problem.
INTERNET & WEB BASED PROGRAMMING (CGI, PERL & HTML)
M.Sc. Bioinformatics Semester II
UNIT I-Internet Basics;The Basics of the Internet, Concepts of a Domain, Networking
concepts, IP Addressing, Resolving Domain Names, Structure of an IP address, Overview of
TCP/IP and its services, The World Wide Web, FTP and Telnet. UNIT II-Hyper text markup language (HTML);How a Web Browser communicates with a
web server, what is HTML and various HTML tags, Commonly used HTML commands, Lists,
Adding Graphics to HTML documents, to create and use Tables, the concept of Hyperlink,
Types of Hyperlinks, Introduction to Frames, Using the <Frameset> and the <Frame> tag. Other
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tags and versions of HTML such as DHTML and XML. UNIT III-Common Gateway Interface (CGI);The concept of CGI, Why CGI is used, How
CGI works, The two methods of Data submissions, the differences in the two methods of
submissions, the importance of Environment variables in a CGI program, the basic steps required
to process from information in a CGI program, Why Perl is the language of choice for
programming in CGI. UNIT IV-Perl Language; The basics of the Perl Language, the concept of Perl Strings and their
types, the values that can be stored in scalar variables, Arrays, how to extract information from
both types of Arrays, the importance of the special Hash Array, Performing operations &
Controlling program Flow, Perl Functions, File Handling. UNIT IV-Perl applications for biological data: BioPerl.
BIOINFORMATICS – II
M.Sc. Bioinformatics Semester III
UNIT I-1.Scoring Models and Matrices;Scoring models for gap penalties, computational
aspects and generation of PAM and BLOSUM matrices. Applications of substitution matrices in
protein sequence alignment and evolution. UNIT II- Markov Chains & Hidden Markov Models;Introduction to Markov chains and
HMM using Markov chains for discrimination of biological sequences.Forward and backward
algorithms.Parameters estimation for HMMs. HMMs for pairwise and multiple sequence
alignments. Profile HMMs. UNIT III-Machine Learning and Bioinformatics;Introduction to various Machine Learning
techniques and their applications in Bioinformatics.Genetic algorithms, Support Vector Machine,
Neural Networks and their practical applications towards the development of new models,
methods and tools for Bioinformatics. UNIT IV-Computational Models in Phylogenetics: Various computational methods of
phylogenetic and molecular evolutionary analysis. Bootstrap and its computational aspects.Tree
of life and molecular clock. Probabilistic models of evolution. Likelihood and maximum
likelihood algorithms and their applications. UNIT V-Computational RNA Structure analysis; Secondary and tertiary structure of RNA.
Various algorithms of RNA folding and their analysis. Energy minimization in RNA folding.
RNA sequence alignment based on secondary structure and its applications in functional
genomics and phylogeny.
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BIOINFORMATICS-III
M.Sc. Bioinformatics Semester III
UNIT I-Prediction of protein structure; Secondary structure: algorithms of Chou Fasman,
GOR methods.Tertiary Structure: basic principles and protocols, Methods to study 3D structure. Protein structure comparison and classification: classes, folds; the concepts in 3D structure
comparison, purpose of structure comparison, algorithms such as FSSP, VAST and DALI.
Principles of protein folding and methods to study protein folding. UNIT II-Visualization of structures using Rasmol or SPDBViewer or CHIME Basic concepts in molecular modeling:, different types of computer representations of molecules. UNIT III-Molecular Dynamics, Molecular modeling and simulations, Homology modeling
UNIT IV-Computer aided drug design (CADD), Molecular Docking.
UNIT V-Systems Biology; Macromolecular interactions: Protein – Protein, Protein – Nucleic
acids, Protein – carbohydrates etc. Gene and protein networks. Top down and bottom up
approaches in systems biology. Computational methods, tools, and databases in systems biology,
their description, analysis and applications to the biological community. Sequence and structure
based methods of predicting protein-protein interactions.
DATA BASE MANAGEMENT SYSTEMS
M.Sc. Bioinformatics Semester III UNIT I-Introduction, data models- Entity Relationship Model, Relational Model
UNIT II-Relational Databases: SQL, Integrity and Security, Relational – Database designs UNIT III-Data Storage and Querying: Storage and File Structure, Indexing and Hashing, Query
Processing, Query Optimization
UNIT IV-Transaction Management: Transactions, Concurrency Control, Recovery System
UNIT V-Database System Architectures, Distributed Databases, Parallel Databases, Data
Warehousing and Data Mining
RECOMBINANT DNA TECHNOLOGY
M.Sc. Bioinformatics Semester III
Unit I-Basics Concepts: DNA Structure and properties; Restriction Enzymes; DNA ligase,
Klenow enzyme, T4 DNA polymerase, Polynucleotide kinase, Alkaline phosphatase; Cohesive
and blunt end ligation; Linkers; Adaptors; Homopolymeric tailing; Labeling of DNA: Nick
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translation, Random priming, Radioactive and non-radioactive probes, Hybridization techniques:
Northern, Southern and Colony hybridization, Fluorescence in situ hybridization; Chromatin
Immunoprecipitation; DNA-Protein Interactions-Electromobility shift assay;
DNaseIfootprinting; Methyl interference assay Unit II-Cloning Vectors;Plasmids; Bacteriophages; M13 mp vectors; PUC19 and Bluescript
vectors, Phagemids; Lambda vectors; Insertion and Replacement vectors; Cosmids; Artificial
chromosome vectors (YACs; BACs); Animal Virus derived vectors-SV-40; vaccinia/bacculo&
retroviral vectors; Expression vectors; pMal; GST; pET-based vectors; Protein purification; His-
tag; GST-tag; MBP-tag etc.; Intein-based vectors; Inclusion bodies; Methodologies to reduce
formation of inclusion bodies; Baculovirus and pichia vectors system, Plant based vectors, Ti
and Ri as vectors, Yeast vectors, Shuttle vectors Unit III-Cloning Methodologies; Insertion of Foreign DNA into Host Cells; Transformation;
Construction of libraries; Isolation of mRNA and total RNA; cDNA and genomic libraries;
cDNA and genomic cloning; Expression cloning; Jumping and hopping libraries; Southwestern
and Far-western cloning; Protein-protein interactive cloning and Yeast two hybrid system; Phage
display; Principles in maximizing gene expression Unit IV-PCR and Its Applications; Primer design; Fidelity of thermostable enzymes; DNA
polymerases; Types of PCR – multiplex, nested, reverse transcriptase, real time PCR, touchdown
PCR, hot start PCR, colony PCR, cloning of PCR products; Tvectors; Proof reading enzymes;
PCR in gene recombination; Deletion; addition; Overlap extension; and SOEing; Site specific
mutagenesis; PCR in molecular diagnostics; Viral and bacterial detection; PCR based
mutagenesis, Mutation detection: SSCP, DGGE, RFLP, Oligo Ligation Assay (OLA), MCC
(Mismatch Chemical Cleavage, ASA (Allele-Specific Amplification), PTT (Protein Truncation
Test). Unit V-Sequencing methods; Enzymatic DNA sequencing; Chemical sequencing of DNA;
Automated DNA sequencing; RNA sequencing; Chemical Synthesis of oligonucleotides;
Introduction of DNA into mammalian cells; Transfection techniques; Gene silencing techniques;
Introduction to siRNA; siRNA technology; Micro RNA; Construction of siRNA vectors;
Principle and application of gene silencing; Gene knockouts and Gene Therapy; Creation of
knock out mice; Disease model; Somatic and germ-line therapy- in vivo and ex-vivo; Suicide
gene therapy; Gene replacement; Gene targeting; Transgenics; cDNA and intragenic arrays;
Differential gene expression and protein array.
JAVA PROGRAMMING
M.Sc. Bioinformatics Semester III
UNIT–I-C++ Vs JAVA, JAVA and Internet and WWW, JAVA support systems, JAVA
environment., JAVA program structure, Tokens, Statements, JAVA virtual machine, Constant &
Variables, Data Types, Declaration of Variables, Scope of Variables, Symbolic Constants, Type
Casting. Operators : Arithmetic, Relational, Logical Assignments, Increment and Decrement,
Conditional, Bitwise, Special, Expressions & its evaluation. If statement, if…else… statement,
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Nesting of if…else… statements, else…if Ladder, Switch, ?operators, Loops – While, Do, For,
Jumps in Loops, Labelled Loops. UNIT–II-Defining a Class, Adding Variables and Methods, Creating Objects, Accessing Class
Members, Constructors, Methods Overloading, Static Members, Nesting of Methods.
Inheritance: Extending a Class, Overriding Methods, Final Variables and Methods, Final
Classes, Finalize Methods, Abstract methods and Classes, Visibility Control. UNIT–III -Arrays: One Dimensional & two Dimensional, strings, Vectors, wrapper Classes,
Defining Interface Extending Interface, Implementing Interface, Accessing Interface Variable,
System Packages, Using System Package, Adding a Class to a Packages, Hiding Classes. UNIT–IV-Creating Threads, Extending the Threads Class, Stopping and Blocking a Thread, Life
Cycle of a Thread, Using Thread Methods, Thread Exceptions, Thread Priority, Synchronization,
Implementing the Runnable Interface. UNIT–V-Local and Remote Applets Vs Applications, Writing Applets, Applets Life Cycle,
Creating an Executable Applet, Designing a Web Page, Applet Tag, Adding Applet to HTML
File, Running the Applet, Passing Parameters to Applets, Aligning the Display, HTML Tags &
Applets, Getting Input from the User.
Semester IV
Project Work Comprehensive Viva-Voce
Seminars
18
Kumaun University, SSJ Campus, Almora
Syllabus forPG DIPLOPMA IN BIOINFORMATICS
(Two Semester Course )
Ist
Semester
Paper and Subject Code
I
PGDBI-1 Paper-I : Fundamentals of
Biological Systems
PGDBI-2
Paper-II : Computational methods
for Sequence analysis.
PGDBI-3 Paper-III : Molecular interactions
PGDBI-4 Paper –IV : Systems biology
PGDBI-5 Practical-I : Biological Databanks and
Sequence analysis
II PGDBI-6
Paper-V : Programming for
Bioinformatics
PGDBI-7 Paper-VI : Genomics
PGDBI -8 Paper- VII : Proteomics
PGDBI -9 Paper-VIII : Molecular modelling &
Computer aided drug
design
PGDBI -10 Practical-II : Computer aided Drug
design
19
Semester
PGDBI-1-FUNDAMENTALS OF BIOLOGICAL SYSTEMS
Unit I :Biology of cells: Cells as a unit of life, structure of prokaryotic and eukaryotic cells.
An overview of organells (Mitochondria, chloroplasts, ER, Golgi, ribosomes, lysosomes and
peroxysomes, nucleus and nucleolus).Differences and similarities in plant and animal cells.
Cellular membrane: structure, transport, channels, carriers, receptors, endocytosis,
membrane potentials.
Unit II:DNA replication; Transcription and Translation.Cell-cell interactions and signal
transductions: Intercellular junctions, signaling by hormones and neurotransmitters;
receptors, G-proteins, protein kinases and second messangers.Protein traffic in cells.
Unit III:Cell Cycle and regulation – Mitosis, Meiosis.Mutation – Types of mutations, types
of mutagenic a gents and their molecular mechanism; DNA repair; Chromosomal types
and structure; Mechanism by which genome undergoes changes, recombination, mutation,
inversion, duplication, and transposition.
UNIT-IV:Molecules of Life: Introduction to carbohydrates-Monosacharides and their
derivatives, Disaccharides, Polysaccharides. Proteins –Structure of aminoacids, Different
levels of organization-Primary, secondary tertiary and Quarternarystructures. Nucleic
acids ; Purines, pyrimidines, Nucleosides and Nucleotides, Different structural form of
DNA, denaturation and renaturation of DNA.Lipids-Structure and function of Fatty acids,
Triacylglycerols, sphingolipids, steroids and glycerophospholipids.Water, small molecules-
Alkaloids, glycosides, phenols, oligopeptides, Flavonoids, and terpenoids
UNIT-V: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.Metabolism of glucose: glycolysis, TCA
cycle, glycogenesis, glycogenolysis and gluconeogenesis, pentophosphate shunt, ETC.
Digestion of protein and protein metabolism, nitrogen balance: transamination, oxidative
deamination and urea cycle. Lipid metabolism: beta oxidation. Interconnection of
pathways,metabolic regulations.
Ist Semester
20
PGDBI-2- COMPUTATIONAL METHODS FOR SEQUENCE ANALYSIS
UNIT-I:Introduction to bioinformatics, Classification of biological databases, Biological
data formats, Application of bioinformatics in various fields. Introduction to single letter
code of aminoacids,symbols used in nucleotides, data retrieval- Entrez and SRS.
UNIT-II: Introduction to Sequence alignment. Substitution matrices, Scoring matrices –
PAM and BLOSUM. Local and Global alignment concepts, Dot plot. Dynamic
programming methodology: Needleman and Wunsch algorithm. Smith– Waterman
algorithm.Statistics of alignment score. Multiple sequence
alignment.Progressivealignment.Database search for similar sequences using FASTA and
BLAST Programs.
UNIT-III:Evolutionary analysis: distances, cladistic and phenetic methods. Clustering
Methods. Rooted and unrooted tree representation. Bootstrapping strategies, Use of
Clustal and PHYLIP.
UNIT-IV:Gene finding methods. Gene prediction: Analysis and prediction of regulatory
regions. Fragment assembly. Genome sequence assembly, Restriction Mapping, Repeat
Sequence finder.
UNIT-V:Concepts of secondary structure prediction of RNA and Protein. Probabilistic
models: Markov chain, Hidden Markov Models-other applications.
.
Ist Semester
PGDBI-3 MOLECULAR INTERACTIONS
UNIT I:Fundamentals of atomic and molecular orbitals:Theory of atomic and molecular
orbitals; Linear combination of atomic orbitals; Quantitative treatment of valency bond
theory and molecular orbital theory; Resonance structures; sigma bonds and Pi-bonds.
UNIT-II:Fundamentals of chemical bonding and non-bonding interactions;Electrovalent
bond, stability of electrovalent bond. Co-valent bond, partial ionic character ofco-
valent bonds.Shape of orbitals and hybridization. Co-ordination bond, Vander Waals
forces; Metallic bond.Molecular geometry- VSEPR Theory.
21
UNIT-III:Folding pathways; Principles of protein folding, hydrophobic interactions,
electrostatic interactions, non-bonded interactions. Beta turns, gamma turns, types of
helices, disulphide bridge.
UNIT –IV: Molecular interactions; protein-protein, protein-DNA, DNA-Drug, Protein-
Lipid, Protein-Ligand, Protein-Carbohydrate interaction, Metalloproteins, Pi. Pi
interactions, C-H…Pi interactions.
UNIT-V:Spectroscopy: Principles, Theory, Instrumentation and Application of UV,
IR, NMR and Circular dichroism (CD) to macro molecules.
Ist Semester
PGDBI-4 -SYSTEMS BIOLOGY
UNIT- I:Introduction to Systems biology; What is Systems Biology? Integrating Networks.
Methods of study: Micro array – definition, types of array, Micro array analysis:
Hierarchical clustering, Self-organizing maps. Applications of Micro Arrays in systems
biology.
UNIT – II:Metabolomics& Metabolic Pathways; Digestion of proteins and protein
metabolism, Transport metabolism, Carbohydrate metabolism – metabolism of glucose –
glycolysis, TC A cycle, glycogenesis, Pentose phosphate shunt, Electron transport,
Interconnection of pathways, metabolic regulation. Translating biochemical networks into
linear algebra.
UNIT – III:Whole cell simulation: Principle and levels of simulation –VirtualErythrocytes,
Pathological analysis. Flux Balance Analysis
UNIT IV:Relationship analysis: Predicting ligand-binding function, Use of gene cluster,
detecting protein – protein interaction.
UNIT – V:Creative Bioinformatics: Novel use for database. Use of EST database –
Unigene, gene discovery, Primer design, Restriction mapping, Position specific cloning,
SNP database, Target identification, Epitope identification.
22
PGDBI-5- PRACTICAL – I - BIOLOGICAL DATABANKS
AND SEQUENCE ANALYSIS
Biological Databanks Sequence Databases, Structure Databases, Specialized Databases
Data retrieval tools and methods
Database file formats
Molecular visualization
Gene structure and function prediction (using GenScan, GeneMark)
Sequence similarity searching (NCBI BLAST)
Protein sequence analysis (ExPASy proteomics tools)
Multiple sequence alignment (Clustal)
Molecular phylogeny (PHYLIP)
Analysis of protein and nucleic acids sequences,
Sequence analysis using EMBOSS or GCG Wisconsin Package
IInd
Semester
PGDBI-6- BIOINFORMATICS PROGRAMMING
UNIT-I:Programming in C:Introduction, Data types, Operators, Expressions, Control
Flow, Structures, Input and Output, Functions, Pointers and References, String
Processing, File Handling
UNIT-II: Programming in C++ :Basic concepts of OOPS-Introduction to C++,C vs C++-
data types, variables, constants, operators and statements in C++ Functions in C++
function prototype-definition-inlinefunctions-overloaded functions.
UNIT- III: Programming in PERL:Introduction, Basic Operators and Control Structures,
Scalars, Lists, Hashes, FileManipulation, Pattern Matching and Regular Expressions,
Subroutines, Text and StringProcessing.
UNIT-IV: Python Programming: Overview, Data structures, Control Flow, Modules, Basic
I/O, Exception Handling, Regular Expressions, File Manipulation, Classes, Standard
library
23
UNIT-V:BioPERL Programming:General Bioperl classes, Sequences (Bio::Seq Class,
Sequence Manipulation), Features and Location Classes (Extracting CDS), Alignments
(AlignIO), Analysis (Blast, Genscan), Databases (Database Classes, Accessing a local
Database)
IInd
Semester
PGDBI-7-GENOMICS
UNIT–I:Definition of Genome, Genome sequencing, Genome map: Types of Genome maps
and their uses, High and low-resolution map, Map elements, Polymorphic markers, Types
of maps: Cytogenetic, Linkage map, Transcript map, Physical map, Comparative map,
Integrated map, STS content maps, Map repositories: NCBI – Entrez Human genome map
viewer, OMIM – Online Mendelian Inheritance in Man, Linkage map resources: CEPH
reference pedigree, CHLC – Cooperative human l inkagecenter, Radiation hybrid map
resources. Practical uses of genome maps: Locating genomic regions, Target identification,
Arrangement of genes, SNP diagnosis, Positional specific cloning,
UNIT–II:Genome Anatomies; The anatomy of the Eukaryotic Genome –The special
features of metaphase chromosomes, where are the genes in the genome? Families of genes,
pseudogenes – Eukaryotic organelle genomes, Repetitive DNA content of the human
genome.Transcriptomes and Proteomes;Genome Expression in outline; The RNA content
of the Cell– the Transcriptome – yeast and human; The Protein content of the cell - the link
between the Transcriptome and the Proteome.
UNIT–III: Annotation of the Genome: Structural annotation (Locating coding regions
and other structural elements of the gene). Various approaches in gene prediction:ORF
prediction, Gene prediction in prokaryotes and eukaryotes, Hidden Markov Model,
Pattern discrimination, Evaluation of gene prediction methods, Prediction of promoter
sequences, Functional annotation: (Prediction of gene function), Employing the similarityin
the sequence, gene family and metabolic pathway. Employing the conserved domain,
Profile and motif comparison, EST Comparison.Analysis of Human Genome.
UNIT–IV:ComparativeGenomics:Purpose and Methods of comparison, Tools for genomic
comparison: Applications of Comparative Genomics, Reconstruction of metabolic
pathway, Predicting regulatory elements, Identifying targets, examination of domain
function, analysis of conserved strings.Genome projects and Model Organism research -
Yeast; Drosophila; C. elegans; and Mouse – a comparative analysis. Comparative genomic
s as an aid to gene mapping and in the study of human diseases.
24
UNIT–V:FunctionalGenomics:Gene expression analysis by cDNA micro arrays, SAGE,
Strategies for generating ESTs and full length inserts; EST clustering and assembly; EST
databases (DBEST, UNIGENE); Expression and regulation of entire set of genes,
Sporulation Vs Vegetative condition in yeast and Bacillus.
IInd Semester
PGDBI-8-PROTEOMICS
UNIT–I:Protein classification: Structural elements and terminology, Helix, Sheet, Strand,
Loop and coil, Active site, Architecture, Blocks, Class and Domains, Fold, Motif, PSSM,
Profile. Principles of classification: Based on structural features, Phylogenetic relationship,
CATH – Classification by Class, Architecture, Topology, Homology, SCOP - Structural
Classification of Protein, FSSP – Fold classification based on structure – structure
alignment, MMDB – Molecular Modeling Data base, SARF – Spatial arrangement of
backbone fragments.
UNIT–II:Protein structure prediction: Use of sequence pattern, leucine zipper, coiled coil,
transmembrane, signal peptide, cleavage site. Secondary structure prediction: Chou –
Fasman / GOR method, Neural network, nearest neighbor method, tertiary structure
prediction, threading profile, contact potential, modeling.
UNIT– II:Analytical protein and peptide separations - Complex protein and peptide
mixtures, Extracting proteins from biological samples, Protein separation before digestion:
1D and 2 D Electrophoresis, Immobilized pH gradient, Sample preparation, First
dimension criteria, second dimension criteria, Stabilization, Detecting protein on gel:
Electro blot, Image analysis, Digital imaging, Spot detection and quantification, Gel
matching. Data Analysis – Database for 2D gel.
UNIT–IV:Tools of Proteomics-Mass Spectrometry for protein and peptide analysis:-
MALDI-TOF Analyzers,-ESI Tandem MS instrument,-Tandem Mass Analyzers,-The
Triple Quadrupole Mass Analyzer,-The Ion Trap Mass Analyzer,-Q-TOF &
Fourier Transform–Ion Cyclotron Resonance MS Instrument,
UNIT–V: Functional Proteome Analysis: Integrated Proteome Analysis - Phage antibody
as tool, Protein expression analysis, High throughput analysis for proteomics. Automation
of proteomic analysis. Proteomics in plant breeding: Objectives,principles and methods,
Genetic diversity analysis, Distribution of varieties, lines andcultivars, Mutant
25
characteristics, Variability between organ and developmental stage, Identification of
abiotic stress, Genetic mapping of protein markers.
IInd
Semester
PGDBI-8-MOLECULAR MODELING & COMPUTER
AIDED DRUG DESIGN
UNIT-I:Introduction to the concepts of molecular modeling. Molecular structure and
internal energy.Application of molecular graphics. Energy minimization of small
molecules: Empirical representation of molecular energies. Use of force fields and the
molecular mechanics method.Discussion of local and global energy minima.
UNIT-II;The techniques of molecular dynamics and Monte Carlo.Simulation for
conformational analysis. Ab initio,dft and semi empirical methods.
UNIT-III: Macromolecular modeling. Design of ligands for known macromolecular target
sites.Principles of Docking studies, Drug – receptor interactions.Classical SAR. / QSAR
studies and their implications to the 3-D modeler. 2-D and 3-D database searching.
Pharmacophore identification and novel drug design.
UNIT-IV:Docking-Rigid and Flexible.Finding new drug targets to treat disease, new
targets foranti-cancer drugs, Drugs that rescue mutant p53’s.
UNIT-V: Structure-based drug design for all classes of targets. EnzymeInhibition
strategies.
PGDBI-10-PRACTICAL II- COMPUTER AIDED DRUG DESIGN
Small molecule building, using ISIS DRAW and CHEM SKETCH
Homology Modeling using SPDBV
Model structure refinement using SPDBV
Model validation using What Check and Pro Check
Docking using DOCK or AUTODOCK or AMBER
26
Price: Rs. 500/-
DEPARTMENT OF BOTAY
KUMAUN UNIVERSITY, SSJ CAMPUS ALMORA
APPLICATION FORM
Form No: ……………………..2-Detail of Bank draft.
1. Course Applied For PG in Bioinformatics2(a) Bank draft No………………
PGDiploma in Bioinformatics2(b) Date ……………………..
2(c) Name of Bank………………..
3. Name of the Applicant
4. Date of Birth :dd/mm/yyyy
5.Sex : Male Female
6. Category: General SC ST OBC
7. Father’s Name
8.Mother’s Name
9. Address for Correspondence
Pin
10. Permanent Address
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Photograph
27
11. Telephone No.
PSTN
Mobile
12.e-mail Address: ---------------------------------------------------------
13. Educational Qualification
Examination Board/University Subject/Specialization Marks/Max
Marks
Marks in
%
High School
Intermediate
Graduation.
Post graduation
Others
14. Other Activities/Achievements (Co-curricular/community service)
S.No. Activity Achievement
Declaration by the Applicant
I hereby declare that all the information given above is correct and nothing has been concealed. I
shall abide by the decisions of the admission committee. Further, if admitted, I pledge to abide
by the rules and norms of discipline of University and will be liable to administrative action if I
am found guilty of a breach of conduct in the campus.
Date :
Place: Signature of the Applicant
Declaration by Parent/Guardian
If my son/daughter/ward Mr./Ms________________________________________
Is permitted admission to above mentioned course, I herby give an undertaking to pay regularly
all his/her charges/dues related to that course. I also undertake the responsibility for his/her
conduct. I shall not claim refund of fee in part or full once the admission has been taken.
Date :
Place: Signature of Parent/Guardian