Hardware Acceleration of Approximate Tandem Repeat Detection

Kód výsledku v IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F00216305%3A26230%2F10%3APU89517" target="_blank" >RIV/00216305:26230/10:PU89517 - isvavai.cz</a>

Nalezeny alternativní kódy

RIV/00216224:14330/10:00048631

Výsledek na webu

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DOI - Digital Object Identifier

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Jazyk výsledku

angličtina

Název v původním jazyce

Hardware Acceleration of Approximate Tandem Repeat Detection

Popis výsledku v původním jazyce

Understanding the structure and function of DNA sequences represents an important area of research in modern biology. Unfortunately, analysis of&nbsp; such data is often complicated by the presence of mutations introduced by evolutionary processes. At the lowest scale, these usually occur in biological sequences as character substitutions, insertions or deletions (indel).&nbsp; They increase the time-complexity of algorithms for sequence analysis by introducing an element of uncertainty, complicating their practical usage.&nbsp; One class of such algorithms has been designed to search for tandem repeats with possible errors - approximate tandem repeats. This paper investigates the possibilities for hardware acceleration of approximate tandem repeat searching and describes a parametrized architecture suitable for chips with FPGA technology. The proposed architecture is able to detect tandems with both types of errors (mismatches and indels) and does not limit the length of detected tand

Název v anglickém jazyce

Hardware Acceleration of Approximate Tandem Repeat Detection

Popis výsledku anglicky

Understanding the structure and function of DNA sequences represents an important area of research in modern biology. Unfortunately, analysis of&nbsp; such data is often complicated by the presence of mutations introduced by evolutionary processes. At the lowest scale, these usually occur in biological sequences as character substitutions, insertions or deletions (indel).&nbsp; They increase the time-complexity of algorithms for sequence analysis by introducing an element of uncertainty, complicating their practical usage.&nbsp; One class of such algorithms has been designed to search for tandem repeats with possible errors - approximate tandem repeats. This paper investigates the possibilities for hardware acceleration of approximate tandem repeat searching and describes a parametrized architecture suitable for chips with FPGA technology. The proposed architecture is able to detect tandems with both types of errors (mismatches and indels) and does not limit the length of detected tand

Druh

D - Stať ve sborníku

CEP obor

JC - Počítačový hardware a software

OECD FORD obor

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Projekt

<a href="/cs/project/GA204%2F08%2F1560" target="_blank" >GA204/08/1560: Bioinformatická a experimentální identifikace nekanonických struktur v genomové DNA</a><br>

Návaznosti

Z - Vyzkumny zamer (s odkazem do CEZ)

Rok uplatnění

2010

Kód důvěrnosti údajů

S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

Název statě ve sborníku

IEEE Symposium on Field-Programmable Custom Computing Machines

ISBN

978-0-7695-4056-6

ISSN

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e-ISSN

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Počet stran výsledku

8

Strana od-do

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Název nakladatele

IEEE Computer Society

Místo vydání

Charlotte

Místo konání akce

Charlotte, North Carolina

Datum konání akce

2. 5. 2010

Typ akce podle státní příslušnosti

WRD - Celosvětová akce

Kód UT WoS článku

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