Dan Gusfield
- DIMACS Center - Rutgers University
- Piscataway, New Jersey
Topic of Discussion
Discrete algorithms that operate on strings provide the closest
intersection between classical theoretical computer science and modern
molecular biology. These well known algorithms, or close relatives, are
at the heart of systems that search sequence databases (DNA or protein),
and use of these databases has become essential in a many subfields of
modern biology. It is natural then that string algorithms have attracted
the attention of many computer scientists entering the field of
computational biology. However, strings provide only a partial reflection
of molecular biology and discrete string algorithms are somewhat
restricted in the kinds of biological questions they can address. While
there are many valid applications for discrete string algorithms in
molecular biology, it is important to understand the limitations as well
as the opportunities. In this lecture I will review some history,
successes, failures, pitfalls and potentials of using string algorithms in
molecular biology. I will pay particular attention to problems of
multiple string comparisons.
dimacs-www@dimacs.rutgers.edu
Document last modified on October 31, 1994