By Mladen Berekovic, Christian Müller-Schloer, Christian Hochberger, Stephan Wong

ISBN-10: 3642004539

ISBN-13: 9783642004537

This e-book constitutes the refereed complaints of the twenty second foreign convention on structure of Computing structures, ARCS 2009, held in Delft, The Netherlands, in March 2009.
The 21 revised complete papers awarded including three keynote papers have been conscientiously reviewed and chosen from fifty seven submissions. This year's certain concentration is decided on strength information. The papers are geared up in topical sections on compilation applied sciences, reconfigurable and purposes, tremendous parallel architectures, natural computing, reminiscence architectures, enery expertise, Java processing, and chip-level multiprocessing.

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Thus, partitioning has a negligible effect on the false positive rate for typical input parameter combinations of a BLASTN search. Throughput can be further improved by deploying several Bloom filters in parallel. Each of the Bloom filters then looks-up a different w-mer in parallel. The disadvantage of this approach is that the total amount of memory for the Bloom filter vectors is of size P⋅m, where P is the number of Bloom filters, each of length m. In the following we present a space-saving Bloom filter architecture that can support several input w-mers and while keeping a vector of length m.

7, the speedup characterizes the performance gain with respect to the throughput for the FIR filter algorithm. The cost increase is related to the gate count of the designs. In the single PE solution of the FIR filter, the 64 iterations are executed sequentially within one PE. 0. Partitioning the algorithm to 2, 4, . . , 64 PEs theoretically enables also a higher throughput by the same factor. The superlinear speedup in case of the processor array implementations is because of the increasing clock frequency for larger numbers of PEs.

The scan operation consists of finding similarities between a particular query sequence and all sequences of a bank. This allows biologists to identify sequences sharing common subsequences, which from a biological viewpoint have similar functionality. Dynamic programming based alignment algorithms whose complexities are quadratic with respect to the length of the sequences can detect similarities between the query sequence and a subject sequence [8]. One frequently used approach to speed up this prohibitively time consuming operation is to introduce heuristics in the search algorithm.

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Architecture of Computing Systems; ARCS 2009 by Mladen Berekovic, Christian Müller-Schloer, Christian Hochberger, Stephan Wong

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