Mapping uniquely occurring short sequences derived from high throughput technologies to a reference genome

Pavlos  Antoniou; Jackie W. Daykin; Costas S.  Iliopoulos; Derrick  Kourie; Laurent Mouchard; Solon P.  Pissis

doi:10.1109/ITAB.2009.5394394

Mapping uniquely occurring short sequences derived from high throughput technologies to a reference genome

Pavlos Antoniou, Jackie W. Daykin, Costas S. Iliopoulos, Derrick Kourie, Laurent Mouchard, Solon P. Pissis

Department of Computer Science

Research output: Chapter in Book/Report/Conference proceeding › Conference Proceeding (ISBN)

16 Citations (Scopus)

Abstract

Novel high throughput sequencing technology methods have redefined the way genome sequencing is performed. They are able to produce tens of millions of short sequences (reads) in a single experiment and with a much lower cost than previous sequencing methods. Due to this massive amount of data generated by the above systems, efficient algorithms for mapping short sequences to a reference genome are in great demand. In this paper, we present a practical algorithm for addressing the problem of efficiently mapping uniquely occuring short reads to a reference genome. This requires the classification of these short reads into unique and duplicate matches. In particular, we define and solve the Massive Exact Unique Pattern Matching problem in genomes

Original language	English
Title of host publication	2009 9th International Conference on Information Technology and Applications in Biomedicine
Publisher	IEEE Press
Pages	1-4
ISBN (Electronic)	978-1-4244-5379-5
DOIs	https://doi.org/10.1109/ITAB.2009.5394394
Publication status	Published - 2009
Event	9th International Conference on Information Technology and Applications in Biomedicine - Larnaca, Cyprus Duration: 05 Nov 2009 → 07 Nov 2009

Conference

Conference	9th International Conference on Information Technology and Applications in Biomedicine
Country/Territory	Cyprus
City	Larnaca
Period	05 Nov 2009 → 07 Nov 2009

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10.1109/ITAB.2009.5394394

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@inproceedings{6e9e36fbd19d448e8f940fb1e4d53d2d,

title = "Mapping uniquely occurring short sequences derived from high throughput technologies to a reference genome",

abstract = "Novel high throughput sequencing technology methods have redefined the way genome sequencing is performed. They are able to produce tens of millions of short sequences (reads) in a single experiment and with a much lower cost than previous sequencing methods. Due to this massive amount of data generated by the above systems, efficient algorithms for mapping short sequences to a reference genome are in great demand. In this paper, we present a practical algorithm for addressing the problem of efficiently mapping uniquely occuring short reads to a reference genome. This requires the classification of these short reads into unique and duplicate matches. In particular, we define and solve the Massive Exact Unique Pattern Matching problem in genomes",

author = "Pavlos Antoniou and Daykin, \{Jackie W.\} and Iliopoulos, \{Costas S.\} and Derrick Kourie and Laurent Mouchard and Pissis, \{Solon P.\}",

year = "2009",

doi = "10.1109/ITAB.2009.5394394",

language = "English",

pages = "1--4",

booktitle = "2009 9th International Conference on Information Technology and Applications in Biomedicine",

publisher = "IEEE Press",

address = "United States of America",

note = "9th International Conference on Information Technology and Applications in Biomedicine ; Conference date: 05-11-2009 Through 07-11-2009",

}

Antoniou, P, Daykin, JW, Iliopoulos, CS, Kourie, D, Mouchard, L & Pissis, SP 2009, Mapping uniquely occurring short sequences derived from high throughput technologies to a reference genome. in 2009 9th International Conference on Information Technology and Applications in Biomedicine. IEEE Press, pp. 1-4, 9th International Conference on Information Technology and Applications in Biomedicine, Larnaca, Cyprus, 05 Nov 2009. https://doi.org/10.1109/ITAB.2009.5394394

Mapping uniquely occurring short sequences derived from high throughput technologies to a reference genome. / Antoniou, Pavlos ; Daykin, Jackie W.; Iliopoulos, Costas S. et al.
2009 9th International Conference on Information Technology and Applications in Biomedicine. IEEE Press, 2009. p. 1-4.

Research output: Chapter in Book/Report/Conference proceeding › Conference Proceeding (ISBN)

TY - GEN

T1 - Mapping uniquely occurring short sequences derived from high throughput technologies to a reference genome

AU - Antoniou, Pavlos

AU - Daykin, Jackie W.

AU - Iliopoulos, Costas S.

AU - Kourie, Derrick

AU - Mouchard, Laurent

AU - Pissis, Solon P.

PY - 2009

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AB - Novel high throughput sequencing technology methods have redefined the way genome sequencing is performed. They are able to produce tens of millions of short sequences (reads) in a single experiment and with a much lower cost than previous sequencing methods. Due to this massive amount of data generated by the above systems, efficient algorithms for mapping short sequences to a reference genome are in great demand. In this paper, we present a practical algorithm for addressing the problem of efficiently mapping uniquely occuring short reads to a reference genome. This requires the classification of these short reads into unique and duplicate matches. In particular, we define and solve the Massive Exact Unique Pattern Matching problem in genomes

U2 - 10.1109/ITAB.2009.5394394

DO - 10.1109/ITAB.2009.5394394

M3 - Conference Proceeding (ISBN)

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BT - 2009 9th International Conference on Information Technology and Applications in Biomedicine

PB - IEEE Press

T2 - 9th International Conference on Information Technology and Applications in Biomedicine

Y2 - 5 November 2009 through 7 November 2009

ER -

Mapping uniquely occurring short sequences derived from high throughput technologies to a reference genome

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