IV - Currents, Cousins, and Cameos

Summary

In the previous three parts of the book we developed general techniques and specific string algorithms whose importance is either already well established or is likely to be established. We expect that the material of those three parts will be relevant to the field of string algorithms and molecular sequence analysis for many years to come. In this final part of the book we branch out from well established techniques and from problems strictly defined on strings. We do this in three ways.

First, we discuss techniques that are very current but may not stand the test of time although they may lead to more powerful and effective methods. Similarly, we discuss string problems that are tied to current technology in molecular biology but may become less important as that technology changes.

Second, we discuss problems, such as physical mapping, fragment assembly, and building phylogenetic (evolutionary) trees, that, although related to string problems, are not themselves string problems. These cousins of string problems either motivate specific pure string problems or motivate string problems generally by providing a more complete picture of how biological sequence data are obtained, or they use the output of pure string algorithms.

Third, we introduce a few important cameo topics without giving as much depth and detail as has generally been given to other topics in the book.

Of course, some topics to be presented in this final part of the book cross the three categories and are simultaneously currents, cousins, and cameos.