COURSE OBJECTIVES

These labs are designed for demonstration of biocomputing techniques with local and remote servers. Student learning occurs when using real data with actual biocomputing software. Students apply theory learned in lecture to experimental settings yielding an advanced understanding of evolution, form, and function.

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


1 Introduction to Biological Databases Expasy, NCBI, Ensemble, Polysearch
2 Sequence Retrieval and Queries FASTA Format, Gene Bank, EMBOSS (dot plot)
3 Sequence Alignment BLAST, SwissProt
4 Sequence Properties Identification GC Content Calculator, PI Value Searching, Molecular Weight using Expasy Tools
5 Multiple Sequence Alignment Tools CLUSTAL OMEGA, CLUSTALW, MUSCLE, T-Coffee
6 Phylogenetic Tree Construction – I CLUSTAL OMEGA, PHYLIP, MEGA5
7 Phylogenetics Tree Construction – II PHYLIP, ReBASE, UniProt
8 Primer Designing Primer3, BiSearch
9 LAB MID TERM
10 RNA Structure and Protein Structure Prediction Translation and Transcription Tools, Modeller
11 Optimization and Visualization Tools Chimera
12 Optimization and Folding Tools Discovery Studio PFam
13 Pathways and Networks STRING KEGG
14 Drug Designing – I Online Tools – PatchDock, SwissDock
15 Drug Designing – II AutoDock