M.Sc in Bioinformatics

Bharathiar University
In Coimbatore

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Important information

  • Master
  • Coimbatore
  • Duration:
    2 Years

Goal. Improve content and utility of chemical-biological databases. Develop better tools and databases for comprehensive functional studies. Develop and improve tools for representing and analyzing sequences similarity and. variations. Create mechanisms to support effective approaches for producing robust,. exportable software that can be widely shared

Important information

Where and when

Starts Location
On request
Bharathiar University, Coimbatore, 641046., Tamil Nadu, India
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Frequent Asked Questions

· Requirements

A pass in any one of the following degree courses of UGC recognized Universities. B.Sc., Agriculture/Animal Biotechnology/Animal science/Applied science/B.Tech - Biotech/Biochemistry/Bioinformatics/Biology/Biotechnology/Botany/Chemistry/ Computer applications/Computer science/Electronics/Environmental science/ Food science/Forestry/Horticulture/Information technology/Mathematics/Medical sciences -

Course programme

Bioinformatics is an emerging scientific discipline representing the combined
power of biology, mathematics and computers. Bioinformatics is needed to handle the
enormous amount of data being generated by researchers identifying the lengthy DNA
sequences of humans, plants, animals and microorganisms-life's blueprint and other
biological data.
Stored digitally, in computers world wide, are trillions of pieces of information
generated by emerging technologies in molecular biology. The amount of public DNA
sequence data doubles every 12-14 months and will increase even more dramatically in the
coming year. The resulting bottleneck-a wedge between having data and knowing what the
data mean-must be overcome to facilitate breakthroughs in medicine, agriculture and
environmental sciences.
Fortunately, biology and computer science are converging to unite raw data with
powerful software tools and mathematical models. Bioinformatics represents a frontier in
biological research and the best path toward finding meaning in a world of complex data.
II Goal
\u0001 Improve content and utility of chemical-biological databases
\u0001 Develop better tools and databases for comprehensive functional studies
\u0001 Develop and improve tools for representing and analyzing sequences similarity and
\u0001 Create mechanisms to support effective approaches for producing robust,
exportable software that can be widely shared
III Bioinformatics and its scope
In last decade, bioinformatics has emerged as a new discipline. Bioinformatics uses
advances in the area of computer science, information science, computer and information
technology to solve complex problems in life sciences and particularly in biotechnology.
Data capture, data ware housing and data mining have become major issues for
biotechnologists and biological scientists due to sudden growth in quantitative data in
biology such as complete genomes of biological species including human genome, protein
sequences, protein 3D structures metabolic pathways databases, cell line and hybridoma
information, biodiversity related information. Advancement in information technology,particularly internet, is being used to gather and access ever increasing information in
biology and biotechnology. Functional genomics, proteomics, discovery of new drugs and
vaccines, molecular diagnostic kits and pharmacogenomics are some of the areas in which
bioinformatics has become an integral part of research and development. The knowledge of
multimedia databases, tools to carry out data analysis and modeling of molecular and
biological systems on computer workstations as well as in a network environment has
become essential for any student of bioinformatics. Bioinformatics, the multidisciplinary
area has grown so much that one divides it into molecular bioinformatics, organal
bioinformatics and species bioinformatics. Issues related to biodiversity and environment,
cloning of higher animals such as Dolly and Polly, tissue culture and cloning of plants
brought out that Bioinformatics is not only a support branch of science, but is also a subject
that directs future course of research in biotechnology and life sciences. The importance
and usefulness of bioinformatics is realized in last few years by many industries. Therefore,
large bioinformatics R&D divisions are being established in many pharmaceutical
companies, biotechnological companies and even in other conventional industries, dealing
with biological. Bioinformatics is thus rated as number one career in the field of
Biosciences. The need of trained manpower in this area is on increase but there are very
few centers in the world where such training is given at present.
In short, bioinformatics deals with database creation, data analysis and modeling.
Data capturing is done not only from printed material but also from network resources.
Databases in biology are generally in the multimedia form organized in relational database
model. Modeling is done not only on single biological molecule but also on multiple
systems thus requiring a use of high performance computing systems.

Course number : 07BIC01 Number of lecture hours: 5
Subject description :
Some basic aspects of Molecular Biology and Genetics that are relevant to the course are
included in this paper.
To understand the basic structure of cell, mechanism and regulation of biological processes
fundamental to genome structure and biochemistry.
Students completing this paper should be able to understand concepts of molecular biology
that are basic to bioinformatics.
Unit I :
Biology of cells: Cells as a unit of life, structure of prokayotic 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 agents and their molecular mechanism;
DNA repair; Chromosomal types and structure; Mechanism by which genome undergoes
changes, recombination, mutation, inversion, duplication, and transposition.
Molecules of Life: Introduction to carbohydrates-Monosacharides and their derivatives,
Disacharides, Polysacharides.
Proteins -Structure of aminoacids, Different levels of organization-Primary, secondary
tertiary and Quarternary structures.
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
Water, small molecules-Alkaloids, glycosides, phenols, oligopeptides, Flavonoids, and
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.

Course number : 07BIC02 Number of lecture hours: 5
Subject description :
This paper describes how to acquire information from biological databases, use of
computational approaches to analyze this information, and interpret the results as a guide to
experiments in biology.
The goal of this course is to introduce the main principles of bioinformatics. The coverage
will include concepts like sequence alignments, phylogenetic trees, and structure
Understand Genomic data acquisition and analysis, comparative and predictive analysis of
DNA and protein sequence, Phylogenetic inference etc.
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.
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. Progressive alignment. Database search for
similar sequences using FASTA and BLAST Programs.
Evolutionary analysis: distances, Cladistic and Phenetic methods. Clustering Methods.
Rooted and unrooted tree representation. Bootstrapping strategies, Use of Clustal and
Gene finding methods. Gene prediction: Analysis and prediction of regulatory regions.
Fragment assembly. Genome sequence assembly, Restriction Mapping, Repeat Sequence
Concepts of secondary structure prediction of RNA and Protein
Probabilistic models:Markov chain, Hidden Markov Models-other applications.

Course number : 07BIC03 Number of lecture hours: 5
Subject description :
This subject presents the fundamentals of programming techniques, namely sequence of
execution, Selection of blocks to be executed, repetition of execution etc with the help of
C programming language.
To make the students to learn problem solving, execution of programs, thinking the
problems in procedure manner and apply the concepts
On successful completion of the course the students should have:
Understood basic of approaching a problem to be computerized
Learnt the various techniques of writing codes to be executed.

Programming in C
Introduction, Data types, Operators, Expressions, Control Flow, Structures, Input and
Output, Functions, Pointers and References, String Processing, File Handling
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-inline
functions-overloaded functions.
Programming in PERL
Introduction, Basic Operators and Control Structures, Scalars, Lists, Hashes, File
Manipulation, Pattern Matching and Regular Expressions, Subroutines, Text and String
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)
Python Programming
Overview, Data structures, Control Flow, Modules, Basic I/O, Exception Handling,
Regular Expressions, File Manipulation, Classes, Standard library
Course number : 07BIE01 Number of lecture hours: 5
Subject description :
This paper includes Basic mathematics and statistics
To learn the basic idea that are essential for a clear understanding of various algorithms and
some techniques.
Students should be able to understand algorithms in sequence analysis, and develops simple
tools in bioinformatics.
Matrix Algebra - Types - Determinants - Transpose - Conjugate - Inverse - Eigen
values of matrices - Rank - Solving Simultaneous equations in three variables using
matrices, Cayley - Hamilton theorem without proof - Verification and Computation of
Inverse of a Matrix - Consistency of linear equations.
Vector - Addtion, subtraction - Dot product - Cross product (up to 3 vectors) - Scalar
triple product - Gradient - Divergence and Curl.
Differentiation - Standard results - Derivatives of simple functions - Product Rule -
Quotient Rule.
Partial Differentiation - Partial derivative of simple functions (3 variables case only) -
Euler's Theorem.
Integration - Standard results - Integrals of simple functions - Definite Integrals -
Indefinite Integrals - Integration by parts - Integration by substitution - Integration by
partial fractions.
Ungrouped data and Frequency distribution: Collection - Classification - Tabulation -
graphical and diagrammatic representation of numerical data - Graphs - Histogram,
Frequency curve.
Statistical Averages: Mean, Median, Mode, SD, Variance and Coefficient of variation.
Correlation and regression analysis: Types of correlation, Methods of studying
correlation - Rank correlation - Simple linear regression - Regression Equations.
Random experiment - Definitions of probability - Theorems of Probability: Addition rule
-Multiplication Rule - Properties of probability - Conditional probability - Bayes Theorem
- Simple Problems.
Random variables - Discrete and Continuous - Probability mass functions - Probability
density functions - Cumulative density function and its properties - Distributions Function.
Theoretical distributions - Binomial, Poisson and Normal distributions - Basic ideas and
their applications.
Sampling: Population - Sample - Parameter - Statistic - Standard error -Hypothesis-Null
Hypothesis - Alternative Hypothesis - Critical Region - Level of Significance - Errors in
Sampling - One tailed and two test statistic-test of significance and its test procedure.
Test of significance for small samples: Tests based on normal distribution for Single
mean, difference of two means - Tests based on t-distribution for single mean, difference of
two means, paired test and observed correlation coefficient - F Test - Parametric and
Non parametric tests - Chi-square (Χ
2) test for goodness of fit.
Analysis of variance: One way and two way classifications.
Course Number : 07BIC04 Number of lecture hours: 5
Subject Description :
This subject presents introduction to GUI, creation of various controls to be used in the
project, connecting databases with the front end etc..
To make the students to learn problem solving using visual basic programming language
As well as connecting front end and back end .
On successful completion of the course the students should have:
Understood GUI programming techniques.
Learnt the various controls used in a program.
Learnt the applications of object oriented approach.
Learnt the connectivity of databases to the controls.
Introduction: Data abstraction, Data models, Instances & schemes E-R Model: Entity and
entity sets, Relations and relationship sets, E-R diagrams, Reducing E-R diagrams to tables.
Network Data Model: Basic concepts, Hierarchical Data Model: Basic concepts.
Introduction to distributed database processing.
Data definition languages - Data Manipulation language, Data Control language, Data and
String Functions, Union and intersect operator, Sub queries, Normal Form, Introduction to
PL/SQL , Data types in SQL, Simple PL/SQL programs.
Visual Basic: Introduction to Client / Server technology, Introduction to Visual Basic
features, Data types, Strings, Variant, Constant, Data Arrays, looping and iterative
Simple controls, Command buttons, text boxes, labels, list box, drive list box, directory list
box, file list box, combo box, check box, timer control, functions in Visual Basic.
Introduction to data connectivity, different database connectivity approaches, simple
connectivity program using data control.
Menu creation, MDI forms, VB scripting, Introduction to ASP.

Course number : 07BIC05 Number of lecture hours: 5
Subject description :
This paper deals with some of the basic features in molecular interactions.
To make the students familiar with chemical bonding and interaction between the
Students should be able to interpret the interaction between molecules.
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; s-bonds and p-bonds.
Fundamentals of chemical bonding and non-bonding interactions:
Electrovalent bond, stability of electrovalent bond. Co- valent bond - partial ionic character
of co-valent bonds. Shape of orbitals and hybridization. Co-ordination bond, Vander Waals
forces; Metallic bond. Molecular geometry- VSEPR TheoryUNIT-III
Folding pathways: Principles of protein folding, role of chaperons, hydrophobic
interactions, electrostatic interactions, non-bonded interactions. Beta turns, gamma turns,
types of helices, disulphide bridge.
Molecular interactions: protein-protein, protein-DNA, DNA-Drug, Protein-Lipid,
Protein-Ligand, Protein-Carbohydrate interaction, Metalloprotein. Pi ... Pi interactions, CH...
Pi interactions.
Spectroscopy: Principles, Theory, Instrumentation and Application of UV, IR, NMR and
Circular dichroism (CD) to macro molecules. Stereochemistry of proteins and nucleic
Course number : 07BIC06 Number of lecture hours: 5
Subject description :
This paper emphasizes the biophysical techniques for 2D and 3D structure prediction.
A thorough understanding of biomolecular structure and function is prerequisite to study
To get an insight into the biophysical techniques to analyze protein molecules
Introduction to protein structure: Physical and chemical properties of aminoacids and
polypeptides. Theoretical and experimental methods for determination of size of proteins.
Physical nature of non covalent interactions. Conformational properties of proteins,
Ramachandarn Plot, Secondary, Super Secondary, tertiary and quaternary structure of
Protein structure modeling: Homology modeling, Threading, Fold recognition, Vectar
based method, neural network. Model refinement and validation. Fuctional classification
of proteins: Cell surface receptors, GPCR's, Kinases, Channel proteins, Ubiquitin
Biophysical Techniques: Principles, Process and Applications of Thin layer
chromatography, Column chromatography ( ion exchange and affinity only) , HPLC, Uni
Directional and 2 D Electrophoresis, UV Visible spectroscopy, NMR and MALDI - TOF
X-ray crystallography of small molecules; x-ray generation ; its application; unit cell and xray
anomalous scattering; lattices, Bragg's Law; atomic scattering factor and structure
factor; phase problem; intensity data collection and reduction; direct method of solving a
small molecule; refinement of crystal structure, hydrogen bonding
X-ray crystallography of macromolecules. Isolation and purification of protein
(chromatography, electrophoresis), crystallization (sitting and hanging drop method).
Protein structure determination-molecular replacement technique; multiple isomorphous
replacement method, synchrotron radiation and its uses; multi wavelength anomalous
diffraction method. Calculation of electron density map, interpretation of electron density
map. Refinement of the structure. Structure validation methods.
Course number : 07BIE02 Number of lecture hours: 5
Subject description :
Basic mathematics pertaining to bioinformatics is included in this paper.
To learn the basic idea that are essential for a clear understanding of various algorithms and
optimization techniques.
Students should be able to understand algorithms in sequence analysis, and develops simple
tools in bioinformatics.
Errors involved in the construction of a mathematical model of the real physical process -
Errors in Numerical Calculations - Errors in the numerical approximation of the
mathematical model (truncation errors) - Errors in a series approximation - Errors in the
actual computation using a computer (round off errors).UNIT-II: MINIMIZATION OR MAXIMATION OF FUNCTION
Problems with Minimum number of iterations
One Dimensional Optimization: Golden section Method, parabolic interpolation and
Brent's method in one dimension, one-dimensional search with first derivatives. Secondorder
Derivative: Newton-Raphson method,
Multidimensional Optimization: Univariate Method - Pattern Diredtions - Powell's
Method - Conjuagate directions - Algorithm - Quadratic Convergence - Downhill simplex
method in multi dimensions, Indirect Search Methods - Gradient - Steepest
decent(Cauchy) method - Conjugate gradient(Fletcher-Reeves) method - Procedure.
Monte-Carlo minimization.
Genetic algorithms - Representation of Design Variables - Representation of Objective
function and Constraints - Genetic Operators.
Simulated annealing - Procedure - Features.
Fourier Transform of Discretely Sampled Data - Discrete convolution - Periodic sequence
and Circular convolution -Linear Convolution through circular convolution -Fast Fourier
Transform(FFT) - Discrete in Time(DIT) - Discrete in Frequency(DIF) - Algorithm -
Computation of inverse DFT - Simple problems.
Solution by Taylor's series Method - Euler's Method - Modified Euler Method - Midpoint
Method, Runge-Kutta Method, Predictor-Corrector Methods - Adam's-Moulton Method -
Milne's Method - Simultaneous and Higher Order Equations, Methods to solve stiff
equations (Implicit Euler Method and Explicit Euler Method).
Subject description :
This paper includes the isolation of protein, nucleic acid and some of the basics in
immunology and pharmacology techniques.
To understand the isolation of biomolecules and techniques related to pharmocolgy and
To make the student to learn the techniques which are basics to bioinformatics.
1. Isolation of Microbes (fungi, bacteria and Actinomycetes) from soil - serial dilution
2. Screening of microbes for enzymes (amylase) production plate and enzyme assay
3. Isolation / Extraction of intracellular and extra cellular enzymes
4. Construction of purification table for any one enzyme
5. Molecular weight determination (SDS - PAGE)
6. Native PAGE and elution of enzyme from the gel
Nucleic Acid Lab
7. Isolation of DNA from microbial and animal cells
8. Isolation of RNA from bakers yeast
9. Isolation of plasmid from bacterium
10. Restriction, digestion and ligation
11. PCR amplification
Immunology lab
12. Methods of bleeding
13. counting of blood cells- Haemocytometre count
14. Preparation of serum from blood
15. Blood grouping- Haemoagglutination
Pharmacology Lab
17. Screening of microbes for antibiotic production
18. Antibiotic bioassay(Kirby Bauer method)
19. Extraction of any one pharmaceutical compound from medicinal plants (soxlet -
extraction method)
20. Tissue culture technique for secondary metabolites production
21. Structure prediction of pharmaceutical compound by NMR
Course Number : 07BIP02 Number of hours: 5
Subject description :
Some of the basic programs in MS- office, HTML, C and perl ,
The use C and Perl and available modules for routinely performed bioinformatics tasks.
Ability to write simple Perl scripts. And develop web page
MS-Office and HTML.
1. Working with MS-Office Packages -One Exercise each in Word, Excel, Power
Point and Access.
2. Working with HTML Tags and HTML Forms. Creating HTML Pages (At least five
different pages to be created using all tags learnt).
3. Basic commands in MS-DOS and command line execution in LI NUX.
Programming in C and PERL
I. Character array manipulations
1) Read and Display a character array
2) Reverse print the array (Sting Reverse)
3) Length of the array
4) Copying the contents of one array to another (String Copy)
5) Copy the Uppercase character of one array as Lowercase character to another
6) Checking whether a string is a palindrome or not
7) Copy the left 'n' characters of one array to another
8) Copy the last 'n' characters of one array to another
9) Copy the middle 'n' characters of one array to another
10) Concatenate two character arrays (String Concatenate)
11) Counting the numbers of Words, Lines and characters in an array
12) Counting the numbers of Uppercase and Lowercase Alphabets, Digits and
special characters in an array
13) Check the number of occurrences of a pattern
14) Check the occurrences of a pattern and skip the same.
15) Check the occurrences of a pattern and replace it with a different pattern
II. Pointers and Character Array
16) Pattern Counting
17) Pattern Skipping
18) Pattern Replacing
III. Files and Command Line Arguments
19) Read data from the keyboard and write it in the file(char by char)
20) Read data from the file and display it on the screen(char by char)
21) Display the content of all the files(Cat all the files)
22) Copy data from one file to another
23) Pattern Count
24) Line in which the pattern occurs with line number
25) Grep all files (Pattern match all the files)
PERL Programming
1. Program to store a DNA sequence
2. Program to concatenate DNA fragments
3. Program to convert DNA to RNA
4. Program to calculate reverse compliment of DNA sequence
5. Program to read protein sequence data from a file
6. Program to print the elements of a array
7. Program to take an element off the end of an array
8. Program to take an element off the beginning of an array
9. Program to put an element at the beginning of an array
10. Program to put an element at the end of an array
11. Program to reverse an array
12. Program to get the length of an array
13. Program to insert an element at a random position in an array
14. Program to find motifs in a protein sequence
15. Program to count nucleotides in a sequence
16 Program to find the percentage of hydrophobic amino acids in a sequence
17 Program to find the percentage of G and C in a DNA sequence
18. Program to append ATGC to a DNA sequence using subroutines
19. Program to concatenate two strings using subroutines
20. Program to count the number of given motifs
21. Program to convert DNAto RNA using subroutines
22. Program to find if a DNA is stable or not
1. Create Tables, queries, and Simple PL/SQL Programs.
2. Construct user interface with manipulation and validation
3. Provide Database Connectivity and hence produce Reports.
Mini project using Visual Basic and RDBMS

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