M. PHIL. BIOINFORMATICS

PAPER I RESEARCH METHODOLOGY THEORY AND TECHNIQUES UNIT - I Research: Definition, Importance and Meaning of research, Characteristics of research, Types of Research, Steps in research, Identification, Selection and formulation of research problem, Research questions – Research design – Formulation of Hypo Dissertation, Review of Literature. UNIT – II Sampling techniques: Sampling theory, types of sampling – Steps in sampling – Sampling and Non-sampling error – Sample size – Advantages and limitations of sampling. Collection of Data: Primary Data – Meaning – Data Collection methods – Secondary data – Meaning – Relevances, limitations and cautions. UNIT – III Statistics in Research – Measure of Central tendency, Dispersion, Skewness and Kurtosis in research, Hypo Dissertation, Fundamentals of Hypo Dissertation testing, Standard Error, Point and Interval estimates, Important Non-Parametric tests: Sign, Run, Kruskal, Wallis tests and Mann, Whitney test. UNIT – IV Para metric tests: Testing of significance, mean, Proportion, Variance and Correlation, testing for Significance of difference between means, proportions, variances and correlation co-efficient. Chi-square tests, ANOVA, One-way and Two-way. UNIT– V Research Report: Types of reports, contents, styles of reporting, Steps in drafting reports, editing the final draft, evaluating the final draft. Reference Books: 1. Statistical Methods - S.P. Gupta 2. Research Methodology Methods and Techniques - C.R. Kothari 3. Statistics (Theory and Practice) - B.N. Gupta 4. Research Methodology Methods and Statistical Techniques - Santosh Gupta PAPER-II BIOLOGICAL DATABASES, DATA MINING AND MICRO ARRAYS UNIT-I Biological database - Sequence databases - Other specialized databases – Microarray databases - Database browsers and search engines. UNIT-II Data mining definition – Classification and clustering of data – Association rules – Data visualization. UNIT-III Introduction to Micoarrys - Oligonucleotide and Spotted cDNA arrays – Design considerations for microarray experiments – Goals of a microarray experiment. UNIT-IV Basic research with DNA microarrays – Micorarrays and Cancer - Myeloid leukemia (AML) vs. acute lymphoblastic leukemia (ALL) data analysis. UNIT-V Use of array analysis programs – SAM - TIGR programs – MEV. References: 1. Analysis of DNA Microarray Data by Steen Knudsen. 2. Discovering Genomics, Proteomics, and Bioinformatics by A.M. Campbell and L.J. Heyer. PAPER-III STRUCTURAL BIOINFORMATICS UNIT I: Structural features of biomolecules – techniques used to determine the structure of biomolecules - geometrical parameters – potential energy surfaces – molecular graphics – hardware and software requirements – Internet – mathematical concepts,molecular file formats UNIT II: Structure prediction – secondary structure – homology modeling, fold recognition and ab initio 3D structure prediction – structure comparison and alignment – prediction of function from structure. UNIT III: Molecular dynamic using simple models – simulations with continuous potentials – advantage of constant temperature and pressure simulation – solvent effects – analysis of conformational changes during molecular dynamic simulation. UNIT IV: Molecular docking – structure based drug design – de novo approach – molecular similarity – quantitative structure-activity relationship – 3D pharmacophore derivation and matching – importance of molecular modeling in drug discovery, Cheminformatics and its applications, Combinatorial libraries and Chemical diversity UNIT V: Protein stability and folding-SCOP-DALI-assignment of protein structures to genomesdetermining gene function through conserved protein structure-prediction of protein functionapproaches to protein structural genomics References: 1. Mount, D.W. (2001).” Bioinformatics – Sequence and Genome Analysis”, 1st Edition, Cold Spring Harbor Laboratory Press, New York, USA. 2. Westhead, D.R., Parish, J.H. and Twyman, R.M. (2003). Instant Notes Series Bioinformatics, 1 st Edition, Viva Books Private Limited, New Delhi, India. 3. Ignacimuthu (s.j.), S. (2005). Basic Bioinformatics, 1st Edition, Narosa Publishing House, New Delhi, India. PAPER-IV DISSERTATION