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Paper Details

%T Application of occam to biological sequence comparisons
%A Shane S. Sturrock, Ian Salmon
%E Janet Edwards
%B Proceedings of WoTUG\-14: Occam and the Transputer\-Current Developments
%X One of the major uses of computers by molecular biologists
   is the alignment of protein or DNA sequences. Since the
   structure and function of proteins and DNA cannot be
   predicted directly from sequence data alone, the most useful
   procedure is to compare unknown sequences against a database
   of known sequences. Those with a high degree of homology are
   likely to have similar properties. At present, the databases
   are growing exponentially with doubling in around 20 months.
   Consequently, comparisons are taking proportionately longer
   to complete. We have applied various sequential comparative
   algorithms within a farming harness constructed in occam
   from a pipeline of transputers. The design of the farming
   harness for optimum link communication is discussed. The
   advantage our method offers is scalability; an important
   consideration as the databases multiply in content. The
   ability to tailor the algorithm to work on various size
   networks of transputers also allows the user to weigh time
   considerations against the total cost of the system. Our
   present implementation can perform around 600 comparisons
   per second between a query sequence of 50 residues and a
   database using 64 worker processors.

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