Contents

• 1 Basics of Multiple Alignment
  • 1.1 What is a Multiple Alignment ?
  • 1.2 The Dynamic Programming Hyperlattice.
  • 1.3 Calculation of a Multiple Alignment by Standard Dynamic Programming.
  • 1.4 Computational Complexity of Multiple Alignment by Standard Dynamic Programming.
  • 1.5 Some Bibliographic Hints.
• 2 The Carrillo-Lipman Method for Optimal Multiple Alignment
  • 2.1 A Visual Explanation of the Carrillo Lipman Bound.
  • 2.2 Mathematical Derivation of the Carrillo-Lipman Bound.
  • 2.3 Where do we go from here ?
  • 2.4 Some Bibliographic Hints.
• 3 Heuristic Alignment Procedures and Examples
  • 3.1 Alignment along a Tree.
  • 3.2 A Hands-On Example: Aligning Immunoglobulin Sequences.
  • 3.3 Getting the Immunoglobulin Sequences from the Internet.
  • 3.4 Optimal, Heuristic, and Structurally Verified Alignments of the Immunoglobulin Sequences.
  • 3.5 Some Bibliographic Hints.
  • 3.6 Appendix 1. Another Heuristic Alignment of the Immunoglobulin Sequences.
  • 3.7 Appendix 2. "Optimal" MSA-Alignment in Fasta-Format.
  • 3.8 Acknowledgement.
• References
• About this document ...

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Georg Fuellen