DNA PATTERN MATCHING ON LOOSELY COUPLED RECONFIGURABLE SYSTEMS

Bibliographic Details
Main Author:	SARELLA, HANANIEL
Language:	English
Published:	University of Cincinnati / OhioLINK 2005
Subjects:	DNA Pattern Matching FPGA Reconfigurable PCI Throughput
Online Access:	http://rave.ohiolink.edu/etdc/view?acc_num=ucin1105408305

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spelling	ndltd-OhioLink-oai-etd.ohiolink.edu-ucin11054083052021-08-03T06:10:00Z DNA PATTERN MATCHING ON LOOSELY COUPLED RECONFIGURABLE SYSTEMS SARELLA, HANANIEL DNA Pattern Matching FPGA Reconfigurable PCI Throughput The explosion of DNA sequence databases necessitates hardware based implementations for managing and querying them. Finding patterns of DNA base-pairs, that are known to control the DNA transcription mechanism, is of considerable interest to the Genome research community. This problem needs a repeated regular structure of low bit-width data paths, working in parallel over a large amount of data. The high performance/cost ratio of FPGA based reconfigurable solutions coupled with their flexibility and adaptability to low bit width data paths make them an ideal platform for these query problems. Of particular interest are Reconfigurable computing processors which use a medium performance coupling mechanism such as the PCI bus to interact with a host microprocessor. These design platforms have the benefits of being cost effective as well as allowing independent processing of computationally intensive parts of the problem. However, they impose constraints on the performance by throttling the throughput because of available bandwidth in the coupling mechanism. This thesis gives the design specification of a solution which will eliminate this bottleneck to provide a high performance solution. The result is compared with a previous implementation without this optimization. 2005-05-27 English text University of Cincinnati / OhioLINK http://rave.ohiolink.edu/etdc/view?acc_num=ucin1105408305 http://rave.ohiolink.edu/etdc/view?acc_num=ucin1105408305 unrestricted This thesis or dissertation is protected by copyright: all rights reserved. It may not be copied or redistributed beyond the terms of applicable copyright laws.
collection	NDLTD
language	English
sources	NDLTD
topic	DNA Pattern Matching FPGA Reconfigurable PCI Throughput
spellingShingle	DNA Pattern Matching FPGA Reconfigurable PCI Throughput SARELLA, HANANIEL DNA PATTERN MATCHING ON LOOSELY COUPLED RECONFIGURABLE SYSTEMS
author	SARELLA, HANANIEL
author_facet	SARELLA, HANANIEL
author_sort	SARELLA, HANANIEL
title	DNA PATTERN MATCHING ON LOOSELY COUPLED RECONFIGURABLE SYSTEMS
title_short	DNA PATTERN MATCHING ON LOOSELY COUPLED RECONFIGURABLE SYSTEMS
title_full	DNA PATTERN MATCHING ON LOOSELY COUPLED RECONFIGURABLE SYSTEMS
title_fullStr	DNA PATTERN MATCHING ON LOOSELY COUPLED RECONFIGURABLE SYSTEMS
title_full_unstemmed	DNA PATTERN MATCHING ON LOOSELY COUPLED RECONFIGURABLE SYSTEMS
title_sort	dna pattern matching on loosely coupled reconfigurable systems
publisher	University of Cincinnati / OhioLINK
publishDate	2005
url	http://rave.ohiolink.edu/etdc/view?acc_num=ucin1105408305
work_keys_str_mv	AT sarellahananiel dnapatternmatchingonlooselycoupledreconfigurablesystems
_version_	1719432039576371200

DNA PATTERN MATCHING ON LOOSELY COUPLED RECONFIGURABLE SYSTEMS

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