BIOINFORMATICS

Sub Code : 07G801 Hrs/week: 4+0+0 Credits : 4 Objective: CIE Marks: 100 Exam: 3 Hrs SEE Marks: 100

1. To understand principles of Bioinformatics and Programming. 2. To understand Biological Databases and Tools that aid in the analysis of Biological data. 3. To use tools such as web interfaces & standalone tools to analyze and interpret the
biological data. 4. To make use of the Perl for the analysis of Biological Data. PART-A 1. Introduction to Biomolecules Introduction to Biomolecules - Types of Biomolecules. Structure, Types and Functions of Carbohydrates, Lipids, Nucleic Acids and Proteins. Genetic code, Codon degeneracy, Genes and Genomes. (04 Hrs)

02. Bioinformatics & Biological Databases Introduction to Bioinformatics, Goals, Scope, Applications in biological science and medicine and Limitations, a) Sequence Databases b) Structure Databases c) Special Databases and applications: Genome, Microarray, Metabolic pathway, motif, multiple sequence alignment and domain databases. Mapping databases genome wide maps. Chromosome specific human maps. Applications of these databases. (05 Hrs) 03. Sequence analysis Sequence Alignment: Evolutionary basis, Homology vs Similarity, Similarity vs Identity. Types of Sequence alignment - Pairwise and Multiple sequence alignment, Alignment algorithms, Scoring matrices, Statistical significance of sequence alignment. Database Similarity Searching: Unique Requirements of Database Searching. Heuristic Database searching, Basic Local Alignment Search Tool (BLAST), FASTA, Comparison of FASTA and BLAST, Database Searching with the SmithWaterman Method. Multiple Sequence Alignment: Scoring function, Exhaustive algorithms, Heuristic algorithms, Practical issues. (08 Hrs) Profiles and Hidden Markov Models: Position-Specific scoring matrices, Profiles, Markov Model and Hidden Markov Model. Molecular Phylogenetics: Phylogenetics Basics. Molecular Evolution and Molecular Phylogenetics - Terminology, Gene Phylogeny vs Species Phylogeny, Forms of Tree Representation. Phylogenetic Tree Construction Methods and Programs - DistanceBased Methods, Character-Based Methods. Phylogenetic Tree evaluation methods. Phylogenetic analysis programs. (07 Hrs)

PART-B 04. Predictive Methods Predictive methods using Nucleic acid sequence - DNA framework, Masking of repetitive DNA, predicting RNA secondary structure, Finding RNA genes, Detection of functional sites and Codon bias in the DNA. Predictive methods using protein sequence - Protein identity and Physical properties. Structure prediction - Prediction of secondary structure of protein, Antigenic sites, Active sites, Folding classes, Specialized structures and Tertiary structures. Gene and Promoter Prediction: Promoter and Regulatory elements in Prokaryotes and Eukaryotes. Promoter and Regulatory element prediction algorithms. Gene prediction.

Gene prediction in Prokaryotes and Eukaryotes. Categories of Gene Prediction Programs. Prediction algorithms. (06 Hrs)
05. Molecular Modeling and Drug Designing Introduction to molecular modeling, methods of molecular modeling. Drug designing process - deriving pharmacophore pattern, receptor mapping, estimating biological activities, ligand-receptor interactions and molecular docking. Drug designing methods such as Rational drug designing and QSAR. (04 Hrs)

06. Perl Programming

Perl - Introduction to Perl, writing and executing a Perl program. Data Types Scalar, Arrays and Associative arrays. Operators, Variables and Special variables. Regular Expressions REGEX operators, Metacharacters and Character classes. Subroutines types of functions, defining and calling functions. Packages writing and calling packages. Modules writing and calling modules. (08 Hrs) BioPerl - Introduction to BioPerl, BioPerl Modules, Applications of BioPerl Sequence retrieval and Sequence submission, Pair wise and Multiple sequence alignment, Restriction mapping, Parsing BLAST/FASTA results, Submitting sequence data to Web forms and retrieving results, Using search reports parsed by SearchIO to obtain robust overall alignment statistics, Bioperl and phylogenetic analysis, BioPerl and Phylogenetic tree manipulation, Creating graphics for Sequence display and Annotation. (06 Hrs) Outcome: Students will be able to apply the principles of Bioinformatics and Programming to the problems of Life sciences such as Sequence analysis, Macromolecular Structural studies, Molecular phylogenetics, Genetic engineering, Genetics, Microbial pathology, Drug designing etc. Reference Books:

1. Jin Xiong. Essential Bioinformatics. Cambridge University Press. 2006. 2. Srinivas Aluru. Handbook of computational molecular biology, CRC Press, 2006. 3. Lukas K. Buehler, Hooman H. Rashidi. Bioinformatics Basics: Applications in Biological
Science and Medicine, 2nd ed. CRC Press. 2005. 4. Arun Jagota. Perl for Bioinformatics. Arun Jagota, 2004. 5. D. C. Young. Computational Drug Design: A Guide for Computational and Medicinal Chemists.Wiley-Interscience, 2009. Scheme of Semester End Examination:

FIVE full questions to be answered out of eight questions; at least TWO out of FOUR questions to be answered from each Part.