Contents

• Contents
• Synopsis
• Abstract
• Introduction
• Alignment of two sequences
  • The scoring scheme, substitution or pair-score matrix
  • Dealing with Gaps
  • Finding the optimal alignment of two sequences
  • Position specific gaps-penalties: Domains and secondary structure
  • Position specific weights: Profile comparison
  • Local alignment algorithm
  • Alternative alignments for the same two sequences
  • Aligning sequences in linear space
  • Comparing sequences without alignment
• Multiple sequence alignment
  • Extending dynamic programming to more than two sequences
  • Hierarchical Methods of Multiple Sequence Alignment
• How well do alignment methods work?
• Software for Sequence and Structure Comparison and Analysis
  • SCANPS - fast local alignment database searching
  • AMPS - pair-wise and multiple alignment of sequences
  • STAMP - multiple alignment from protein 3D structure comparison
  • AMAS - Analysis of Multiply Aligned Sequences
  • ALSCRIPT - annotation and colouring of a multiple sequence alignment
  • OC - general hierarchical cluster analysis
• Figure Legends
  • FIGURE 1
  • FIGURE 2
• Bibliography