Bioinformatics BITO-215

1. BioinformaticsBITO-215 Ayesha Masrur Khan 9th Feb, 2012

2. Course Outline Introduction to Bioinformatics • Definition of Bioinformatics and Related Fields • Earliest Bioinformatics Efforts • Objective and Scope of Bioinformatics • Kind of Data Used in Bioinformatics • Introduction to Databases • Major Biological Databases Sequence Alignment • Pairwise Sequence Alignment • Database Similarity Searching • Multiple Sequence Alignment • Profiles and Hidden Markov Models • Protein Motifs and Domain prediction Introduction

3. Course Outline..contd. Gene and Promoter Prediction • Gene Prediction • Methods of Gene Prediction • Gene Prediction tools • Promoter and Regulatory Element Prediction • Promoter and Regulatory Element Prediction Tools Molecular Phylogenetics • Phylogenetic Basics • Phylogenetic Tree Construction Methods and Programs • Phylogenetic Tree Evaluation Structural Bioinformatics • Protein Structure Basics • Protein Structure Visualization, Comparison and Classification • Protein Structure Visualization Tools • Protein Secondary Structure Prediction • Protein Tertiary Structure Prediction • Protein Structure Prediction Tools • RNA Structure Prediction Methods and Tools Introduction

4. Course Outline..contd. Genomics and Proteomics • Introduction to Genomics • Tools for Genome Analysis • Genome Mapping, Assembly and Comparison • Functional Genomics • Introduction to Proteomics • Tools for Proteome Analysis • Advanced topics • Molecular dynamics simulation • Computational drug design • Microarray data analysis Introduction

5. Recommended Books • Introduction to Bioinformatics, by T. K. Attwood and D.J. Parry-Smith (2006) Pearson Education, Ltd. (available at the library, a few copies will be made for your benefit) • Introduction to Bioinformatics: A Theoretical and Practical Approach, by Stephen A. Krawetz and David D. Womble. • Essential Bioinformatics, by Jin Xiong(2006) Cambridge University Press. Introduction

6. Course Assessment Assignment: 10% Quizzes: 10 % Sessional-1: 15 % Sessional-2 (project + presentation): 20% Terminal Exam: 45% Note: Project and assignments should be submitted on the assigned due date. No late submissions or extension requests will be accepted. Introduction

7. Central Paradigm of Molecular Biology Introduction

8. Central Paradigm of Bioinformatics Introduction

9. What is Bioinformatics? • Information technology applied to the management and analysis of biological data. • It was originally coined in the mid-1980s for the analysis of biological data. • It can include computational manipulation and analysis of biological sequence data, as well as manipulation and analysis of three-dimensional structural data. • What laid the foundation of this revolutionary field? • Protein sequencing and Nucleic acid sequencing in the 60’s and 70’s paved the way for sequence revolution and hence the 80’s saw progress in computer-based technologies to cope with this surge in information Introduction

10. Related fields Systems Biology Proteomics: Study of the entire complement of proteins (proteome) Structural Genomics: Pursuance of protein structures on a genome wide scale. Genomics: Study of genomes of organisms. Systems Biology: Studies the complex systems which exist within and across multiple biological scales Introduction