Contents

• 1 Distance and Similarity
  • 1.1 Introduction
  • 1.2 Alphabets and Sequences
  • 1.3 Edit Distances
    • Some Exercises involving Edit Distances
• 2 Pairwise Alignment via Dynamic Programming
  • 2.1 Calculating Edit Distances and Optimal Alignments
    • Some Exercises involving Dynamic Programming
  • 2.2 A Word on the Dynamic Programming Paradigm
  • 2.3 A Word on Scoring Functions and Related Notions
• 3 Weight Matrices for Sequence Similarity Scoring
  • Some Exercises involving Weight Matrices
• 4 Realistic Gap Models
  • Some Exercises involving Gap Cost Models
• 5 Variations of Pairwise Alignment
  • 5.1 Local Alignment and Local Similarity
    • Some Exercises involving Local Alignment / Local Similarity
  • 5.2 Heuristic Methods
    • Some Exercises involving Heuristic Methods
• 6 Appendix
  • 6.1 The DNA alphabet
  • 6.2 The extended genetic alphabet
  • 6.3 The single-letter amino-acid code
  • 6.4 Abstract alphabets
  • 6.5 Some examples of taking subsequences
  • 6.6 Some simple properties of subsequences
  • 6.7 Metric axioms
  • 6.8 Ambiguity of optimal alignment
• 7 Some Recommended Reading
• References
• About this document ...

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Robert Giegerich