B.Tech. (BT) VI Semester
Course Code : EURBT 601 Category: BE
Credits: 3 Hours : 3 per week
Introduction to Biological databases. Brief introduction to types of information
available in different biological databases (details to be covered in practicals).
Fragment assembly. Gene prediction – Statistical and similarity based approaches.
Sequence analysis: introduction. Similarity matrices – PAM and BLOSUM.
Searching databases using BLAST. Description of the BLAST algorithm.
Pairwise sequence alignment using dynamic programming. Needleman & Wunsch
algorithm for global alignment. Smith-Waterman algorithm for local alignment.
Dynamic programming for sequence alignment with affine gap penalties. Searching
for repeats and partial overlaps using dynamic programming.
Phylogenetic analysis. Distance based methods: UPGMA and Neighbor joining.
Classical parsimony and weighted parsimony methods. Branch and bound.
Multiple sequence alignment. Multidimensional dynamic programming. Progressive
alignment and profile alignment. Sankoff and Cedergren method for Simultaneous
alignment and phylogeny.
Prediction of secondary structure from protein sequence – Chou-Fasman rules, neural
Prediction of transmembrane helices.
Prediction of protein conformation from protein sequence. Information theoretical
methods: Homology and threading. Basic Concepts of prediction using Force fields –
Energy minimization, molecular dynamics and simulated annealing.
1. Bioinformatics: Sequence and Genome analysis by D.Mount. 2nd ed. 2005. CBS
2. Biological sequence analysis: Probabilistic models of proteins and nucleic acids by
Durbin, Eddy, Krogh and Mitchison. 1998 Cambridge University Press.
3. Molecular modeling: principles and applications. A. Leach. 2nd ed. 2001. Pearson.
1. Molecular modeling and simulation: Tamar Schlick.(2002) Springer-Verlag.
2. Bioinformatics: a practical guide to the analysis of genes and proteins. Baxevanis
3rd Ed. (2004) Wiley.