%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.
If you have any comments on this database, including inaccuracies, requests to remove or add information, or suggestions for improvement, the WoTUG web team are happy to hear of them. We will do our best to resolve problems to everyone's satisfaction.
Copyright for the papers presented in this database normally resides with the authors; please contact them directly for more information. Addresses are normally presented in the full paper.
Pages © WoTUG, or the indicated author. All Rights Reserved.
Comments on these web pages should be addressed to: www at wotug.org