B. Tech Biosciences and Bioengineering

BT 302 Bioinformatics 2-0-2-6

Syllabus: Introduction to biological databases: collection, organization, storage and retrieval of data; Concept of homology and definition of associated terms; Pairwise sequence alignment: dynamic programming algorithm, global (Needleman-Wunsch) and local (Smith-Waterman) alignments; BLAST Scoring matrices (PAM and BLOSUM families), gap penalty, statistical significance of alignment; Multiple sequence alignment: progressive alignment, iterative alignment, sum-of-pairs method, CLUSTAL W; Pattern recognition in protein and DNA sequences, Hidden Markov Model, Profile construction and searching, PSI-BLAST; Big data analysis: introduction to next-generation sequencing analysis, RNA-seq, CHIP-seq, introduction to phylogeny: maximum parsimony method, distance method (neighbor-joining), maximum-likelihood method; Gene prediction in prokaryotes and eukaryotes, homology and ab-initio methods; Genome analysis and annotation; Comparative genomics, cluster of orthologous groups.

Texts:

1. M. Zvelebil and J. O. Baum, Understanding Bioinformatics. Garland Science, 2007.

2. D. W. Mount, Bioinformatics: Sequence and Genome Analysis, 3^rd Edition, CSH Press, 2005.

3. P. E. Bourne, Structural Bioinformatics, 2^nd Edition, Wiley, 2009.

4. R. Durbin, S. R. Eddy, A. Krogh and G. Mitchison, Biological Sequence Analysis, Cambridge University Press, 1998.

References:

1. S. G. Kochan and P. Wood, UNIX Shell Programming, 3^rd Edition SAMS, 2003.