An algorithm for mapping short reads to a dynamically changing genomic sequence

Kód výsledku v IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F68407700%3A21240%2F10%3A00177976" target="_blank" >RIV/68407700:21240/10:00177976 - isvavai.cz</a>

Výsledek na webu

<a href="http://dx.doi.org/10.1109/BIBM.2010.5706551" target="_blank" >http://dx.doi.org/10.1109/BIBM.2010.5706551</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.1109/BIBM.2010.5706551" target="_blank" >10.1109/BIBM.2010.5706551</a>

Jazyk výsledku

angličtina

Název v původním jazyce

An algorithm for mapping short reads to a dynamically changing genomic sequence

Popis výsledku v původním jazyce

The constant advances in sequencing technology have redefined the way genome sequencing is performed. They are able to produce tens of millions of short sequences (reads), during a single experiment, and with a much lower cost than previously possible. Due to this massive amount of data, efficient algorithms for mapping these reads to reference sequences are in great demand, and recently, there has been ample work for publishing such algorithms. In this paper, we study a different version of this problem: mapping these reads to a dynamically changing genomic sequence. We propose a new practical algorithm, which employs a suitable data structure that takes into account potential dynamic effects (replacements, insertions, deletions) on the genomic sequence. The presented experimental results demonstrate that the proposed approach can be applied to address the problem of mapping millions of reads to multiple genomic sequences.

Název v anglickém jazyce

An algorithm for mapping short reads to a dynamically changing genomic sequence

Popis výsledku anglicky

The constant advances in sequencing technology have redefined the way genome sequencing is performed. They are able to produce tens of millions of short sequences (reads), during a single experiment, and with a much lower cost than previously possible. Due to this massive amount of data, efficient algorithms for mapping these reads to reference sequences are in great demand, and recently, there has been ample work for publishing such algorithms. In this paper, we study a different version of this problem: mapping these reads to a dynamically changing genomic sequence. We propose a new practical algorithm, which employs a suitable data structure that takes into account potential dynamic effects (replacements, insertions, deletions) on the genomic sequence. The presented experimental results demonstrate that the proposed approach can be applied to address the problem of mapping millions of reads to multiple genomic sequences.

Druh

D - Stať ve sborníku

CEP obor

IN - Informatika

OECD FORD obor

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Projekt

<a href="/cs/project/GA201%2F09%2F0807" target="_blank" >GA201/09/0807: Analýza a zpracování řetězců a stromů</a><br>

Návaznosti

P - Projekt vyzkumu a vyvoje financovany z verejnych zdroju (s odkazem do CEP)

Rok uplatnění

2010

Kód důvěrnosti údajů

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

Název statě ve sborníku

2010 IEEE International Conference on Bioinformatics and Biomedicine

ISBN

978-1-4244-8305-1

ISSN

—

e-ISSN

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Počet stran výsledku

4

Strana od-do

133-136

Název nakladatele

IEEE Computer Society

Místo vydání

Los Alamitos

Místo konání akce

Hong Kong

Datum konání akce

18. 12. 2010

Typ akce podle státní příslušnosti

WRD - Celosvětová akce

Kód UT WoS článku

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