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Paper Details

  title = "{A}pplication of occam to biological sequence comparisons",
  author= "Sturrock, Shane S. and Salmon, Ian",
  editor= "Edwards, Janet",
  pages = "181--190",
  booktitle= "{P}roceedings of {W}o{TUG}-14: {O}ccam and the {T}ransputer-{C}urrent {D}evelopments",
  isbn= "90 5199 063 4",
  year= "1991",
  month= "sep",
  abstract= "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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