Fundamentals of Bioinformatics - Ogurtsov, A.N. 2013



Introduction

Foundations of Bioinformatics

Subject of Bioinformatics

Characteristics of Bioinformatics Data

Subject Matter of Bioinformatics

Goals and Objectives of Bioinformatics

Future Prospects of Bioinformatics Applications

Bioinformatics Infrastructure

Computer Components of Bioinformatics

Internet Components of Bioinformatics

Bioinformatic Data, Networks, and Databases

Biological Sequences

Information in Molecular Biology

Biological Sequence Alignment

Biological sequences

Dot matrix of similarity

Examples of Data Comparison

Biological Classification and Nomenclature

Examples of Bioinformatic Analysis

Searching for Similar Sequences in Databases

The Concept of "Information"

Definition of the Concept of "Information"

Amount of Information

Properties of Information

The concept of "information"

Genetic information

Genomes and Proteomes

Genomics

Basics of Bioinformatics

Genome Mapping

Foundations of Bioinformatics

DNA Sequencing Methods

Proteomics

Protein Structure and Information

Bioinformatics in Medicine

Methods of Bioinformatic Analysis

Substitution Matrices

Sequence Similarity Measure

Weights of Edit Operations

PAM Matrices

BLOSUM Matrices

Methods of Bioinformatics Analysis

Calculating Sequence Alignment Scores

Methods of Bioinformatic Analysis

Sequence Alignment Algorithms

Dynamic Programming Algorithm

Global Alignment Algorithm

Local Alignment Algorithm

Approximate Methods for Rapid Database Searching

Significance of Alignments

Multiple Sequence Alignment

Visualization of Alignment Results

Methods for Multiple Alignment

Hidden Markov Models

Methods of Bioinformatics Analysis

Phylogenetic Analysis

Homology

Methods of Bioinformatic Analysis

Phylogeny and Phenetics

Methods of Bioinformatics Analysis

Cladistic Methods

Tools for Phylogenetic Analysis

Information Principles in Biotechnology

Sequencing of Biological Sequences and Gene Expression

Open Reading Frame

Biological Sequence Sequencing and Gene Expression

Sequence Determination

Expressed Sequence Tags

Sequencing of Biological Sequences and Gene Expression

Gene Expression

Analysis of Protein Expression

Utilization of Sequencing Results

Genome Function and Organization

Challenges in Gene Analysis

Gene Localization in the Genome

Prokaryotic Genomes

Eukaryotic Genomes

Genome Analysis

Single Nucleotide Polymorphisms

Genome Composition

Horizontal Gene Transfer

Comparative Eukaryotic Genomics

Protein Analysis and Prediction

The Challenge of Protein Structure Decryption

Prediction of Protein Secondary Structure

Prediction of 3D Protein Structures

Protein Prediction Software

Challenges in Protein Function Prediction

Bioinformatics in Pharmacy

Medical Genomics and Pharmacogenomics

Global Pharmaceutical Industry

Drug Discovery and Development

Pharmacoinformatics

Computational Toxicology and Immunoinformatics

List of Abbreviations

References