COURSE OBJECTIVES

This course introduces bioinformatics concepts and practice. Topics include: biological databases, sequence alignment, gene and protein structure prediction, molecular phylogenetics, genomics and proteomics.

COURSE LEARNING OUTCOMES (CLO)

CLO: 1. Comprehend the fundamental principles of Bioinformatics
CLO: 2. Understand the basic concepts and application of Bioinformatics tools to solve biological problems
CLO: 3. Illustrate an determine different biological structures from sequence from databases.

COURSE CONTENTS


• Introduction and Review of Molecular Biology
• Concept of Gene and DNA
• Central Dogma of Molecular Biology
• Introduction to Bioinformatics
• Bioinformatics as an integrative approach
• Application of Bioinformatics and Biosciences
• Introduction to Biological databases
• Biological Databases and Tools
• Literature Databases (PubMed)
• Nucleotide Database (GeneBank, EMBLE)
• Protein Database (PDB, SwissProt)
• Biological Search Engine (Entrez)
• Sequence Homology
• Local and Global Alignment
• Dot Plot
• Dynamic Programming Approach
• Heuristic Approach (BLAST)
• Sequence Homology
• Heuristic Approach (BLAST)
• Multiple Sequence Alignment (CLUSTALW, tCoffee, OMEGA, MUSCLE)
• Genome Visualization
• Introduction to Sequence Components
• Promoters Identification
• UCSC Genome Browser
• ENSEMBLE
• Primer Designing in INSILICO PCR
• PCR Types and Applications
• Primer3 Tool Usage
• Primer Designing in INSILICO PCR
• INSILICO PCR by UCSC Browser
• Phylogenetic Analysis
• Sequence Alignment and Phylogenetic Trees
• Tree Construction, Analysis (PHYLIP, ReBASE, UniProt)
• Protein Structure Bioinformatics
• Introduction to Proteomics
• Primary structure retrieval and databases
• Protein Structure Prediction
• Secondary structure study, tools and analysis
• 3D structure construction, tools and visualization
• Protein Structure Visualization and Optimization
• Proteins Folding Identification Tools – Pfam
• Protein structure visualization and Optimization tools (Chimera)
• Protein-Protein Interaction Tools and Analysis – STRING
• Biological Pathways and Pathways Analysis – KEGG, SMPD