M.Sc., Bioinformatics (CBCS)
(For the students admitted during the academic year 2004-2005)
Scheme of examination
(With project work) - (CBCS – Bharathiar University Department)

Semester II:

Paper I: Advanced Network Technologies
Internet and TCP/IP, Routing, Network Architectures, Web server application development using CGI/PERL and JAVA-socket programming and servelets, Transmission characteristics, Computing environments, Computer and Network security, Network Management systems.

Paper II: Numerical Methods and Optimization Techniques
Numerical Methods and Optimization, Minimization and Maximization of Functions – Golden search, Parabolic interpolation, Brent's method, One-dimensional search with first derivatives, Downhill Simplex method in multi dimensions, Powell's method, Conjugate gradient method, Randomized minimization techniques – Monte Carlo minimization, Simulated annealing, Genetic Algorithm, Fourier Transform, Integration of Ordinary Differential Equations – Runge-Kutta, Taylor's series, Euler's method, modified mid point method, Predictor Corrector Method (Adam's and Milne's Method), Implicit Euler Method and Explicit Euler Method.

Paper III: Structure and Function of Biomolecules
Introduction to protein structures, Theoretical and Experimental methods for determination of size of proteins, Conformational properties of proteins, Ramachandaran plot, various structure of proteins, X-ray crystallography of small molecules, X-ray crystallography of macromolecules, Protein structure modeling, Functional classification of proteins.

Paper IV: Molecular Interactions
Fundamentals of Chemical Bonding and non-bonding interactions, Fundamentals of atomic and molecular orbitals, Pi…Pi interactions, C-H…Pi interactions, Folding pathways, Applications of UV, IR, NMR and Circular Dichroism to macromolecules, Stereochemistry of proteins.

Practical II:
Gene structure and function prediction (GenScan, Genemark), Sequence similarity search (NCBI BLAST), Protein sequence analysis (ExPASy proteomics tools), Multipe sequence alignment (Clustal), Molecular phylogeny (PHYLIP), Analysis of protein and nucleic acids sequences, Sequence analysis using EMBOSS or GCG Wisconsin Package, Development of programs in the analysis of nucleic acid sequences, programs to calculate potential energy of regular structures.