Last modified on 29 December 2006.

The purpose of this section is to increase its readers' knowledge about and awareness of comparative methods by providing:

• a conceptual introduction to comparative sequence analysis, presented from a historical perspective;
• a description of methods designed and used for comparative sequence analysis;
• illustrative examples of how base pairs are assigned; and
• overviews of various RNA molecules studied using comparative methods.

Contents:

• Introduction: Rationale and Methods
• Paradigms and Algorithms
  • Visual Methods
  • The Number Pattern Method
  • Chi-Square Statistical Algorithms
  • Phylogenetic Algorithms
  • Empirical Algorithms
  • Collective Scoring
• Reference Links
  • Current Structure Models for Reference Organisms
  • Structure Definitions