M.Sc.

BIOINFORMATICS SYLLABUS

BIOINFO 501 BIOLOGICAL CHEMISTRY 4+0 Sem. I

Origin of life. Water as the universal biological solvent; concept of osmolarity; Carbohydrates:
monosaccharides, oligosaccharides, polysaccharides, proteoglycans and glycoproteins; Lipids: fatty
acids, acylglycerols; phospholipids, sphingolipids, cholesterol and membranes; isoprenoids,
eicosanoids, and their biological importance; Proteins: amino acids and peptides; primary, secondary,
tertiary and quaternary structures; structure, function and evolutionary relationships; protein – protein
interactions; protein folding; allosteric proteins; Nucleic acids : bases, nucleotides, RNA and DNA;
different structural forms of DNA; denaturation, renaturation and hybridization of DNA; different types of
RNA; protein-nucleic acid interaction; Enzymes: details of enzyme nomenclature and classification;
units of enzyme activity; coenzymes and metal cofactors; temperature and pH effects; Michaelis-
Menten kinetics; Inhibitors and activators; active site and catalytic mechanisms; covalent and non-
covalent regulations; isoenzymes; osmolytes and intracellular modulation of enzymes; Organization of
metabolic systems : enzyme chains, multienzyme complexes and multifunctional enzymes; anaplerotic
sequences and amphibolic pathways; pacemaker enzymes and feedback control of metabolic
pathways; shuttle pathways; energy charge; Oxidation of glucose in cells : high energy bond, glycolysis,
citric acid cycle and oxidative phosphorylation

BIOINFO 502 STATISTICS FOR BIOINFORMATICS 4+0 Sem. I

Calculus: Limits, Complete Differentials, Partial differentials of functions, Integration: Definite and non-
definite integral, Logarithms, Ordinary differential equations (first order), Partial differential equations -
example from biology, Vector - Addition, subtraction, dot, cross, scalar triple product, divergence, curl
of a vector, equation of normal; Matrix algebra: Addition, subtraction, multiplication, transpose inverse,
and conjugate of matrix, Boolean logic; Addition, subtraction, multiplication and division using binary,
octal and hexadecimal systems, Introduction to principles of statistical sampling from a population;
Random sampling; Frequency distributions and associated statistical measures; Probability
Distributions; Correlation and regression analysis; Multivariate analysis; Hypothesis testing; Markov
Models; Cluster Analysis - Nearest neighbour search, Search using stem numbers, Search using text
signatures; Phylogenetic Analysis Tools: Maximum Likelihood, Parsimony methods

BIOINFO 503 CONCEPTS IN COMPUTING 2+2 Sem. I

Fundamentals of Computing; Introduction to operating Systems: WINDOWS, NT, UNIX/Linux operating

systems; Comparative Advantages of Security (hacking, cracking) Installation, Portability and
Programming of these operating systems; Computer Viruses; Use of INTERNET & WWW; Searches on
MEDLINE, CD, bibliographic databases, Graphics: Visualization techniques - Software and Hardware,
Interactive Graphics; Viewing in three dimension; Raster algorithms;; Surface and solid modeling;
Rendering; Animation; Image Processing with stress on biological systems; 3-D image reconstruction

Computer Networking - LAN, WAN, MODEM; Optical Vs. Electronic Networking; Security of the
network, Fire-walls; Network Goals; Applications Network; Network structure; Network architecture;
Hierarchical networks; Ethernet and TCP/IP family of protocols; Transport protocol design
Practical: Exercises on Windows, Linux, UNIX, Networking, Internet search and Grpahics

BIOINFO-504 INTRODUCTIONS TO DATABASE SYSTEMS 2+2 Sem. I

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; Multimedia Databases - Basic Concepts and
Applications; Indexing and Hashing; Basic concepts (ISAM, B+ Tree indexed files, B Tree indexed files,
Static Hash functions, Dynamic Hash functions); Text Databases; Introduction to Distributed Database
Processing, Data Security.
ORACLE

Relational database design; Oracle objects - Tables, Views, Indexes, Sequences; Synonyms,
Snapshots, Database - Tablespace, Datafiles, Blocks, Extents, Segments; Oracle Background
Processes, control files; Oracle Memory Management; Security, Grants, Roles, Privileges; DBA -
Oracle Server Manager; Export-Import/SQL Monitor Backup & Recovery (Archiving); Physical Storage
& Logical Storage; Oracle-Reports - Reports Features; Full Integration with Forms and Graphics; Data
Model and layout editors; Layout Objects - Frames, Repeating Frames, Fields, Boiler Plate, Anchor;
Interface Components; Report Formats; Example Reports; Single Query, Multi Query, Matrix,
Master-Detail etc.; User Defined Columns; PL/SQL Interface; Calling Report from a Form

SQL

Select Statements; Data Definition Statements; Data Manipulation Statements; Data Control
Statements; Other Database Objects (Views, Sequences, Synonyms); Introduction to Application
Development using Visual Basic; Working with Code and Forms; Variables, Procedures and Controlling
Program Executor; Standard Controls; Data Access Using Data Control; Connecting to Oracle
Database using Visual Basic

Practical: Practical exercise using ORACLE and SQL, Design of database in Oracle

BIOINFO 505 COMPUTATIONAL BIOLOGY 2+2 Sem. II

Internal and external co-ordinate system; Generation of co-ordinates of biopolymers in Cartesian and
cylindrical polar co-ordinate system; Methods of single crystal X-ray Diffraction of macromolecules:
molecular replacement method and direct method - Fiber diffraction, Analysis of structures and
correctness of structures, Submission of data to PDB: atomic coordinates and electron density maps;
Anatomy of Proteins - Ramachandran plot, Secondary structures, Motifs, Domains, Tertiary and
quaternary structures; Anatomy of DNA: A, B, Z DNA, DNA bending etc.; RNA structure; Structure of
Ribosome; Principles of Protein Folding; Structural data banks - Protein Data Bank, Cambridge small
molecular crystal structure data bank; Calculation of conformational energy for bio-macromolecules;
Methods for Prediction of Secondary and Tertiary structures of Proteins - Knowledge-based structure
prediction, Fold recognition, Ab initio methods for structure prediction; Methods for comparison of 3D
structures of proteins; Methods to predict three dimensional structures of nucleic acids, rRNA;
Electrostatic energy surface generation; Molecular Mechanics & Molecular Dynamics of Oligopeptides,
Proteins, Nucleotides, & small Molecules - Mechanics and dynamics of bio-macromolecules, Simulation
of molecular mechanics and dynamics, Simulations of Free Energy changes, Force fields; Molecular
interactions of - Protein – Protein, Protein – DNA, Protein – carbohydrate, DNA – small molecules etc.;
Docking of Molecules; Molecular Design

Practical: Usage of software for above topics

BIOINFO 506 GENETICS AND IMMUNOLOGY 3+0 Sem. II

Genetics - Science of genetics – objectives, terminologies, methods; Mendelian principles of

inheritance, sex linked inheritance; Concept of linkage, linkage maps and recombination; Mutations –
molecular, gene/point and chromosomal; Phenotype and genotype relationships, role of environment,
from gene to phenotype, gene interactions. Study of quantitative traits. Genetics of populations,
genetics and evolution. Genetics and diseases

Immunology - Overview of immune system, innate and acquired immune system; Structure and
function of antibody molecule and TCR; Genetics of antibody diversity; MHC I & II, Polymorphism;
Characteristics of B Cell and T Cell antigens; MHC Peptide interaction; Affinity maturation;
Autoimmunity and molecular mimicry; Ligand- receptor interaction in the light of protein structure in
immune system; Use of bioinformatics in immunology and vaccine development
BIOINFO 507 PROGRAMMING LANGUAGES FOR BIOINFORMATICS 2+2 sem. II

Programming in C: Pointers, pointers to functions, macro and programming in C, graphs, data structure
– linked list, stack, queue, binary trees, threaded binary trees, File and exception handling in C

Programming Visual Basic: Introduction to Application Development using Visual Basic; Working with
Code and Forms; Variables, Procedures and Controlling Program Executor; Standard Controls; Data
Access Using Data Control; Connecting to Database

Practical: Programming in C and Visual basic with special reference to database linking

BIOINFO 508 BIOLOGICAL DATABANKS, DATA MINING 1+2 Sem. II

Data warehousing, data capture, data analysis; Introduction to Nucleic Acid and Protein Sequence Data
Banks; Nucleic acid sequence data banks: Genbank, EMBL nucleotide sequence data bank, AIDS
Virus sequence data bank, rRNA data bank, Protein sequence data banks: NBRF-PIR, SWISSPROT,
Signal peptide data bank; Database Similarity Searches: BLAST, FASTA, PSI-BLAST algorithms; Pair
wise sequence alignment - NEEDLEMAN and Wunsch, Smith Waterman algorithms; Multiple sequence
alignments - CLUSTAL, PRAS; Patterns, motifs and Profiles in sequences: Derivation and searching;
Derived Databases of patterns, motifs and profiles: Prosite, Blocks, Prints-S, Pfam, etc.; Primer Design

Practical: Use of similarity, homology and alignment softwares mentioned above.

BIOINFO 509 BIODIVERSITY INFORMATICS 2+1 Sem. II

Biological information; Biological diversity of life; Species diversity: taxonomic information on plants,
animals, microbes and viruses; Genetic diversity; Ecological/ Ecosystem diversity; Urban biodiversity;
Methods for species identification & classification

Biodiversity Databases - Organizing biological species information; Datasets in biodiversity informatics:

Species 2000, Tree of life, ATCC, NBII, Species analyst collaboration, ICTV, Animal Virus Information
System etc.

Practical: Software for identification - Accessing existing databases on the World-wide Web; Software
for identification of species; Probabilistic and deterministic identification; Delta, MicroIS, AVIS, ICTV;
Biocomplexity issues in biodiversity; Need of metadata standards & ontology

BIOINFO 510 BIMOLECULAR SEQUENCING AND ANALYSIS 2+1 Sem. III

Analysis of protein and nucleic acid sequences, multiple alignment programs, Development of
programs for analysis of nucleic acid sequences, Use of GCG package, Conversion of various file
formats, Use of Molecular Modeling package(s), programs to calculate potential energy of regular
structures and their visualization, Use of curve, NUPARM, NEWhelix etc.

Practical: GCG, file formats and molecular modeling softwares.

BIOINFO 511 MOLECULAR MODELLING 1+1 Sem. III

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 MM methods, Local and global energy minima. Techniques in MD and Monte
Carlo. Simulation for conformational analysis, Ab initio, DFT and semi-empirical methods, Design of
ligands, Drug-receptor interactions, Classical SAR/QSAR, 2D and 3D data searching.

Practical: RASMOL, MOLMOL, Chimera, Hyperchem and other MM/MD software

BIOINFO 512 PROGRAMMING IN PERL AND HTML, XML 1+2 Sem. III

PERL: Strings, Numbers, and Variables. Variable Interpolation, Basic Input and Output, File handles,
Making Decisions, Conditional Blocks, Loops, Combining Loops with Input, Standard Input and Output,
Finding the Length of a Sequence File, Pattern Matching, Extracting Patterns, Arrays, Arrays and Lists,
Split and Join, Hashes, A Real-World Example, BioPERL; Applications

HTML/XML: Creation, hosting and maintenance of web-site using HTML and XML, ASP and JSP.

Practical: Web-based application, interactive web-pages,

BIOINFO 513 GENOMICS AND PROTEOMICS 2+1 Sem. III

Genomics - Genome sequencing technology, Whole genome analysis, Comparative genomics -

Paralogs and orthologs, Phylogenetic profiling, Pathway analysis, Repeat analysis, Human genetic
disorders, Candidate gene identification, Linkage analysis, Genotyping analysis, Concepts of
Pharmacogenomics

Proteomics - Introduction to basic Proteomics technology, Bio-informatics in Proteomics, Gene to

Protein Function: a Roundtrip, Analysis of Proteomes, Analysis of 2-D gels, Protein to Disease and Vice
Versa, Human Genome and science after Genome era.

Practical: Analytical softwares related to Genomics and proteomics

BIOINFO 514 NUMERICAL METHODS AND OPTIMIZATION TECHNIQUES 2+0 Sem. III

Numerical methods and optimization: errors involved in the construction of a mathematical model of the
real physical process, errors in the numerical approximation of the mathematical model (truncation
errors), errors in actual computation using a computer (round off errors); Minimization or maximization
of functions: Golden selection search in one dimension, parabolic interpolation and Brent’s method in
one dimension, one dimensional search with first derivatives. Downhill Simplex method in
multidimensions, Direct Set (Powell’s) methods in multidimensions, Conjugate gradient methods in
multidimensions. Fourier transformation: FT of discretely sampled data, fast Fourier ransform; Runge-
Kutta Method, Adaptive step-wise control of Runge-Kutta, Modified mid-point method and other related
methods; methods to solve Stiff Equations

BIOINFO 515 CHEMOINFORMATICS 1+1 Sem. III

Role of computers in chemical research; Structure representation; Chemical Databases – Design,

Storage & Retrieval methods, 2D and 3D structures, reaction databases, search techniques (Full, Sub
and Super structure), similarity searches; Modelling of small molecules; Structure Activity
Relationships; Analysis & Design of combinatorial libraries; Chemoinformatics tools for drug discovery

Practical: AMBER, Advanced HYPERCHEM and MM/MD applications

BIOINFO 516 COMMERCIAL BIOINFORMATICS 1+2 Sem. IV

Definition of Bioinformatics company. Genome Technology: high throughput sequencing and assembly.
Microarray and genome wide expression analysis: transcriptomes, proteome: Genomics in medicine,
disease monitoring, profile for therapeutic molecular targeting. Diagnostic drug discovery and
genomics. Pharmacogenomics and its application. SNPs and their applications. Proteomics in medicine
and its applications. Patenting and data generation from patent literature for commercial benefits. IPR
and bioinformatics. Bioinformatics patents.

Practical: Practical sessions on above topics

BIOINFO 517 MICROARRAY ANALYSIS 1+1 Sem. IV

Introduction to basic micrroarray technology, Bioinformatics in micrroarrays, Getting started - target

selection, Customised microarray design, Image processing and quantification, Normalization and
filtering, Exploratory statistical analysis, Public Microarray data resources

Practical: Software of Microarray analysis – design, processing and analysis

BIOINFO 599 Project 0+5 Sem. IV

BIOINFO 591 Seminar 0+1 Sem. III/ IV

PGS-595 Library Services and Technical writing 1+0 Sem. III/ IV