Bioinformatics

Contents

1. Introduction to Bioinformatics

1. History and Development of Bioinformatics

1.1 Introduction

1.2 What is Bioinformatics?

1.3 Branches of Bioinformatics

1.4 Aims of Bioinformatics

1.5 Scope of Bioinformatics

1.6 Application of Bioinformatics

1.7 Historical background

2. Relation of Bioinformatics with Biotechnology

2. Biological Databases

1. Introduction

2. Types of Biological Databases

2.1 Importance of Biological Databases

3. Nucleic Acid Databases (NCBI, DDBJ, GENBANK and EMBL)

3.1 NCBI

3.2 DDBJ

3.3 GENBANK

3.4 EMBL

4. Protein Databases (PDB, Swiss-Prot, Uniprot)

4.1 PDB

4.2 Swiss-Prot

4.3 Uniprot (The Universal Protein Resource)

5. Structure Databases

5.1 The Structural Classification of Proteins (SCOP)

5.2 PDBsum

6. Literature Databases

6.1 Pubmed

6.2 MEDLINE

3. Data Generation Tools

1. Introduction

2. What is Data Generation?

2.1 Storage and Retrieval of Data

2.2 Significance of Data Generation

2.3 Basic Tools of Data Generation

2.4 Next Generation Sequencing (NGS)

3. NGS Application

3.1 NGS Platforms

3.2 Workflow of NGS Data Analysis

3.3 Handling of NGS Data

4. Protein Sequencing

4.1 Determination of Amino Acid Composition

4.2 Sequence-Alignment Methods

4.3 Multiple-Sequence Alignment

4.4 Phylogenetic Analysis

4.5 Protein Properties and Structure Prediction

4.6 Protein vs Domain Classification

4.7 Protein Superfamily

5. NMR Spectroscopy

6. Microarray

6.1 Applications

6.2 Identification of Differentially Expressed Genes

4. Retrieval of Data

1. Introduction

2. Classification of Data

2.1 Objectives

2.3 Types of Classification

5. Sequence Alignments and Visualization

1. Introduction

1.1 Sequence Alignment

1.2 Dynamic Programming

2. Local Alignment and Global Alignment

2.1 Needleman-Wunsch Algorithm

2.2 Smith-Waterman Algorithm

6. Protein Structure and Visualization Tools

1. Introduction

2. Structure of Proteins

3. Visualization Tools

3.1 SPDBV/ Swiss-PdbViewer or DeepView

3.2 Pymol