Bioinformatics

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Contents

• Foreword
• Introduction

• Part One: Molecular Biology
  1. The central dogma of molecular biology
  2. DNA structure
  3. RNA structure
  4. Protein & Nucleic acid
  5. Human Genome

• Part Two: Sequence Searches and Alignment
  1. Sequence Databases
  2. Nucleic Acid Search Algorithms
  3. Nucleic Acid Alignment Algorithms
  4. Protein Alignment Algorithms

• Part Three: Phylogenetics
  1. Understanding Phylogenetic Trees
  2. Distance Algorithms
  3. Parsimony Algorithms
  4. Likelihood Algorithms
  5. Bayesian Algorithms

• Part Four: Genomics
  1. Whole Genome Assembly
• Part Five: Gene Expression
• Part Six: Protein Structure
  • • Protein Folding
    • Protein structure prediction
      • Secondary structure prediction
      • Homology modelling
      • De novo structure prediction
      • Contact Prediction
    • CASP
• Part Seven: Proteomics
• Part Eight: Metabolomics
• Part Nine: Metagenomics

• Part Ten: Biological sequences and biological diversity
  1. Chemical diversity, arising from sequence diversity, allows biological diversity
  2. How biological complexity is expressed in genomic differences
  3. Biological sequence data indicate a common ancestor for all living things
  4. Unique features of biological sequences derived from extremophiles
  5. The genetic origins of oxygen adapted life, mitochondria and chloroplasts
  6. The genetic origins of multi-cellularity
  7. A living species is defined as much by genetic diversity as by the genome of any particular individual
  8. How genetic variability within a species allows for speciation

• Part Eleven: Other types of biological data
  1. Medical informatics
  2. Environmental or population data
  3. Morphological data
  4. Relational databases and biological data

• Glossary