Bioinformatics II

Inference problems and techniques for molecular biology. Overview of key inference problems in biology: Homology identification, Genomic sequence annotation (Genes and ORFs identification), Protein structure prediction (Secondary and Tertiary structure prediction), Protein function prediction, Biological network identification, Next generation sequencing, Microarray data analysis

Basics of RNA Structure prediction and its limitations, Features of RNA Secondary Structure, RNA structure prediction methods: Based on selfcomplementary regions in RNA sequence, Minimum free energy methods, Suboptimal structure prediction by MFOLD, Prediction based on finding most probable structure and Sequence co-variance method. Application of RNA structure modeling

Decision tree induction, Artificial Neural Networks, Hidden Markov Models, Genetic Algorithms, Simulated Annealing, Support vector machines; The relation between statistics and machine learning; Evaluation of prediction methods: Parametric and Nonparametric tests, cross-validation and empirical significance testing (empirical cycle), Clustering (Hierarchical and Kmean).

Basic concept of Force field in molecular modeling (Potential energy calculation); Overview of key computational simulation techniques: Introduction to simulation, Computer simulation techniques, Types of computer simulation (Continuous, Discrete-event and Hybrid simulation), Differential equation solvers, Parameter estimation, and Sensitivity analysis.

Overview of key techniques for the management of large document collections and the biological literature: Document clustering, Information retrieval system; Natural Language Processing: Introduction, Major areas of NLP, Natural language information extraction; Insilico Drug Designing: Major steps in Drug Designing, Ligand and Structure based drug designing, Protein-ligand docking, QSAR Modeling, Pharmacodynamics (Efficacy & Potency) &Pharmacokinetics (ADME), Lipinski’s rule of five, Pharmacogenomics. B.Tech. (Biotechnology) 3rd Year Dr. A.P.J. Abdul Kalam Technical University Uttar Pradesh, Lucknow