daemon@ig.UUCP (12/01/87)
From: Sunil Maulik <MAULIK@BIONET-20.ARPA>
Computers and the Sequencing of Large Genomes
Searching the database is not, however, a problem really suited to von
Neumann machines. At present the use of so-called 'fine-grained' general
purpose parallel processor machines such as the Transputer (UK) or Connection
Machine (US) appear to be best suited to such problems not only because of
their very high speed in dealing with problems that can be posed
appropriately but because of their flexibility and cheapness. Adapting
programmes such as FASTN or FASTP if optimum efficiency isn't an initial
necessity, would be an almost trivial problem for the Connection Machine, a
somewhat more troublesome exercise for the Transputer. In addition the
modularity of such machines allows them to be built in virtually any size.
Moreover, the fact that these fine grained instruments are near first
generation commercial efforts and are deliberately designed using non-exotic
components clearly indicates that the aspects of simple searches and data
storage can be dealt with quite easily.
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