\title{Fast Matching of CBG Patterns with\\ Applications to Protein
  Matching\thanks{This paper appeared in the roceedings of the
      Thirteenth Symposium of the Pattern Recognition of Association
      of South Africa, Langebaan, South Africa, November 2002,
      pp. 35--40.}}


\author{Scott Hazelhurst and Gloria Aikhorin\\
School of Computer Science\\University of the Witwatersrand, 
Johannesburg\\
Private Bag 3, 2050 Wits, South Africa }


\begin{document}





\begin{abstract}
  The large data set sizes produced in many biological applications,
  makes pattern matching in computational biology a challenge. We
  present a technique for pattern matching an important class of
  protein patterns. We show how such a protein pattern can be
  represented as a logical expression, from which a circuit can be
  automatically synthesised, and implemented on field programmable
  gate arrays, which leads to highly parallelisable solutions. The
  method was tested on the Prosite database, and almost all the
  patterns could be dealt with very efficiently leading to throughput
  rates in most cases excess of $10^8$ symbols per second.
\end{abstract}