Last modified on 10 January 2000.

A Historical Perspective with a Molecular Context:

The goal of this comparative sequence analysis is to determine the common structure shared by different sequences. Over the last twenty years, various algorithms have been developed to help elucidate this common structure. The "Paradigms and Algorithms" section will guide the reader through the significant developments in comparative analysis since its inception by describing the basis of each of these algorithms and providing examples of each algorithm in action. As comparative methods have been used to study more molecules, the methods have improved, biases have been removed, and more information becomes available as the end result. We feel it important to emphasize how much was done at the very beginning, and thus come to appreciate fully the current depth of the information gained from comparative analysis.

tRNA was the first molecule to be studied using comparative methods. Due to this historical significance, we will present examples from tRNA throughout this section to provide a common perspective on comparative sequence analysis. Three alignments were used in the generation of these figures and data:

  • tRNA-895: contains 895 Type 1 tRNA sequences;
  • tRNA-30: a subset of tRNA-895 with only 30 sequences; and
  • tRNA-5: a subset of tRNA-30 with only 5 sequences.
Since tRNA is small (~76 nucleotides), these figures will aid you in understanding material without overwhelming you with information. The secondary structure (in PostScript format) of tRNA will provide context for certain examples.

Next Section: Visual Methods.