Details of LS4205 (Spring 2020)

Level: 4 Type: Theory Credits: 4.0

Course CodeCourse NameInstructor(s)
LS4205 Bioinformatics Anirban Banerjee,
Babu Sudhamalla

(1) Introduction to bioinformatics: Definitions, Different terms used in bioinformatics. Biological databases: Sequence (nucleic acids, proteins) and Structural databases, different file formats to store sequences. Query and retrieval of data from biological databases.

(2) Sequence alignment: Evolutionary basis of sequence alignment, Statistical significance of an alignment. Algorithms for sequence analysis - Global alignment (Needleman-Wunsch), Local alignment (Smith-Waterman), and heuristic-based approaches (BLAST).

(3) Bioinformatics tools: pairwise sequence alignment, multiple sequence alignment, Prediction of exon, intron, promoter region, etc. Prediction of protein secondary and tertiary structure. Homology modeling and molecular docking.

(4) Evolutionary Inference from sequence data: Estimating rates of evolution. Phylogenetic analysis: Fundamental elements in phylogenetic models; tree interpretation. Phylogenetic data analysis, Phylogenetic tree construction, etc. Jukes and Cantor model; Kimura's two-parameter model; Tajima and Nei's method.

(5) Genome analysis: Technologies for large-scale gene expression, Computational tools for expression analysis. Exploration of trends in high-throughput data using Principal Component Analysis (PCA) and hierarchical clustering; differential gene expression using moderated t-test and Receiver Operating Characteristic (ROC); Gene set (pathway) enrichment analysis; gene networks. Basic probability and statistics for sequence analysis.

. Biological Sequence analysis by Durbin, Eddy, Krogh, Mitchison(Cambridge University Press, 1998.
2. Fundamentals of Molecular Evolution by Dan Graur and Wen-Hsiung Li (Sinauer, 2000, Second Edition).
3. Bioinformatics: Sequence and Genome Analysis by David W Mount (Cold Spring Laboratory Press 2004, Second Edition).
4. A. D. Baxevanis and B. F. F. Ouellette, Bioinformatics: A Practical Guide to Analysis of Genes and Proteins

Course Credit Options

Sl. No.ProgrammeSemester NoCourse Choice
1 IP 2 Elective
2 IP 4 Elective
3 IP 6 Not Allowed
4 MR 2 Not Allowed
5 MR 4 Not Allowed
6 MS 8 Elective
7 RS 1 Elective
8 RS 2 Elective