Bio-Informatics - - Syllabus

Paper – 1 computer programming

Unit 1. Introduction to Computers

1.1   Basic principles and concepts of a computers

1.2   Introduction to Disk operating systems

1.3   Windows and word processing

1.4   Basics of MS office

1.5   Concepts of Web Designing

Unit 2. C Language

2.1 Introduction to languages, Procedural language

2.1 C language, Programming concepts in C

2.2 Object oriented programming

2.4 Data types, loops and procedures, Data structures

2.5 Functions, Arrays, Pointers, Strings 

Unit 3. Oracle

3.1 Computational tools for creation maintenance, curation of databases

3.2 PL/SQL basics, SQL functions and procedures, Functions and packages, triggers

3.3 ORACLE objects – sequences, snap shots

3.4 Transaction control and locking : DEAD lock, security, grants, Roles

3.5 SQL navigators, large objects

3.6 Web server programs

Unit 4. Bio Perl

4.1 Introduction to Bio-Perl

4.2 Concepts in Bio-Perl

4.3 Programming in Bio-Perl

Paper II – Biological Databases and Sequence Analysis

Unit 1.   Biological Databanks

1.1   DNA databanks, GENBANK

1.2   Protein sequence Databanks, Swissport, PIR


1.4   Functional motif Databases, PROSITE

1.5   Brookhaven protein databank (PDB)


Unit 2    Information Retrieval

2.1 Information retrieval from databases

2.2 Database querying, key work searching, search machines

2.3 Homology searches

2.4 Pattern matching

Unit 3    DNA sequence Analysis 

3.1 Concepts of DNA/Protein sequence Analysis

3.2 Importance of sequence alignments, Heuristic methods BLAST, FASTA

3.3 Fragment and map assembly and combinatorial approaches to sequencing

3.4 Pair wise sequence alignment versus Multiple sequence alignment

3.5 Correlation of protein sequence and its function

Unit 4    Molecular Phylogenetics

4.1 Tree of life, Phylogeny and Molecular evolution

4.2 Phylogenetic analysis using Phylip

4.3 Distance matrix methods, Character based methods

Paper III Biochemistry, Immunology and Molecular Biology

Unit 1.   Biomolecules and their propertie 

1.1   Principles of Thermodynamics

1.2   Chemical nature of biological reactions

1.3   Concepts of free energy

1.4   Signature of coupled reactions

Unit 2.   Structure and functions of proteins

2.1 Primary, Secondary, tertiary and quaternary structures of proteins

2.2 Forces influencing protein structure

2.3 Structure and functional relationship of enzymes

2.4 Kinetics of enzyme catalyzed reactions

Unit 3.   Immunology

3.1 Basic concepts of immunology

3.2 Cell and hormone mediated immune response

3.3 Antibody diversity and major histo-compatibility complexes

3.4 Autoimmune responses

Unit 4.   Molecular Biology

4.1 Prokaryotic eukaryotic genome structures

4.2 Gene – Protein interactions

4.3 DNA repair and recombination

4.4 Gene mapping and genetic linkages

Paper IV               Genomics, Protein Modeling, Drug Designing

Unit 1.   Protein Structure and Predictions

1.1   Secondary structure prediction methods

1.2   Tertiary structure prediction methods

1.3   Fold recognition

1.4   Homology/Comparative modeling of proteins

1.5   Composer and SITEID

Unit 2.                   Computational Methods

2.1 Energy calculations, local and global minimization

2.2 Energy minimizations: Conjugate, steepest and powell

2.3 Molecular dynamics and simulation studies

Unit 3.                   Drug Designing and Molecular Modeling

3.1 Docking algorithms

3.2 Rational Drug Designing

3.3 Ligand based drug designing

3.4 Dynamics and simulation methods


Unit 4.                   Genomics and Proteomics

4.1 Gene structure predictions

4.2 Structural and functional genomics

4.3 Gene annotation

4.4 2-Dimentional gel electrophoresis for separation and identification of proteins

4.5 Protein – Protein interactions using yeast two hybrid system

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