SCHOOL OF BIOTECHNOLOGY, CHEMICAL & BIOMEDICAL ENGINEERING

Vellore 632 014, Tamil Nadu, India.

Computational Biology LTPC: 3 0 0 3 1.0.0 Computer programming and Analytical Bioinformatics Students will learn about the computational problems in the emerging areas of Bioinformatics, Computational Biology, and Genomics. The students will have varied backgrounds of engineering, computer science, and the life sciences. Expected Outcome: Students can able to understand i) Design mathematical concepts involved in biology ii)Able to develop a algorithm for analysis of biological sequences. Unit No. 1 Introduction Number of hours: 9 Is the genome like a computer program? How the genome is studied, maps and sequences, specific techniques, the human genome project, sequence databases. Strings, graphs, and algorithms Unit No. 2 Sequence Comparison and Database Search Number of hours: 9 Comparing two sequences, global comparison the basic algorithm, database search, pam matrices, blast, fast, other issues, similarity and distance, parameter choice in sequence comparison, string matching and exact sequence comparison. Unit No. 3 Fragment Assembly of DNA Number of hours: 9 The ideal case, complications, alternative methods for DNA sequencing, shortest common superstring, reconstruction, multicontig, algorithms, representing overlaps, paths originating superstrings, shortest superstrings as paths, heuristics, finding overlaps, ordering fragments, alignment and consensus . Unit No. 4 Physical Mapping of DNA Number of hours: 9 Restriction site mapping, hybridization mapping, models, restriction site models, interval graph models, the consecutive ones property, algorithmic implications, an algorithm for the cp problem, an approximation for hybridization mapping with errors, a graph model, a guarantee, computational practice, heuristics for hybridization mapping. Unit No. 5 Phylogenetic Trees Number of hours: 9 Character states and the perfect phylogeny problem, binary character states, two characters, parsimony and compatibility in phylogenies, algorithms for distance matrices, reconstructing additive trees, reconstructing ultrametric trees, agreement between phylogenies. Text Books Joo Meidanis & Joo Carlos Setubal PWS Publishing Company, Boston. 1997 References 1. Konopka, Andrzej K Konopka, M James C Crabbe Compact Handbook Of Computational Biology- Science 2004. 2. Dan Gusfield Algorithms on Strings, Trees, and Sequences: Computer Science and Computational Biolog - Computers - 1997 3. Michael S Waterman Introduction to Computational Biology: Maps, Sequences, and Genomes by - Science - 1995 Mode of Evaluation Announced and Unannounced Quizzes, Assignments/ Seminars and Written Examination. Recommended by the Board of 13th November 2008 Studies on Date of Approval by the Academic Council Version No. Course Prerequisites Objectives:

Proceedings of the 16th Academic Council held on 25.11.2008