BT-5103/BT-5205

Syllabus

Pairwise & Multiple Sequence Alignment

Pairwise sequence similarity: Alignment score and substitution matrices, Gap penalty, Dot plots, The Needleman-Wunsch algorithm, Global and Local Alignment, Types of homology, Database search for sequence similarity (BLAST algorithm, Significance of a hit). Multiple Sequence Alignment: Utility, Progressive & Iterative algorithms, Scoring schemes, Domain search: Position-specific scoring matrix, Hidden Markov Models, PSI-BLAST, InterproScan.

Phylogenetic Analysis

Phylogenetic analysis: Uses, selection of types of sequences, Distance Based (UPGMA, Fitch-Margoliash, and Neighbour joining algorithms), Maximum Parsimony and Maximum likelihood method, determining the quality of phylogenetic trees

Structural Bioinformatics

Secondary structure prediction, Neural networks, Signal peptide prediction. Tertiary Structure Prediction: Homology modelling, Quality Parameters, PDB file format, SwissPDB viewer. Structure-Based Drug Design: Scoring Functions and Molecular Docking.

Books