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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

Pin

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