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

P Antoniou; J Daykin; Costas Iliopoulos; D Kourie; L Mouchard; Solon Pissis

doi:10.1109/ITAB.2009.5394394

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

P Antoniou, J Daykin, Costas Iliopoulos, D Kourie, L Mouchard, Solon Pissis

Informatics

Research output: Chapter in Book/Report/Conference proceeding › Conference paper

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	ITAB 2009
Subtitle of host publication	9th International Conference on Information Technology and Applications in Biomedicine, 2009
Place of Publication	Piscataway, N.J.
Publisher	IEEE
Pages	N/A
Number of pages	4
Volume	N/A
Edition	N/A
ISBN (Print)	9781424453795
DOIs	https://doi.org/10.1109/ITAB.2009.5394394
Publication status	Published - 2009

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10.1109/ITAB.2009.5394394

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Antoniou, P., Daykin, J., Iliopoulos, C., Kourie, D., Mouchard, L., & Pissis, S. (2009). Mapping uniquely occurring short sequences derived from high throughput technologies to a reference genome. In ITAB 2009: 9th International Conference on Information Technology and Applications in Biomedicine, 2009 (N/A ed., Vol. N/A, pp. N/A). IEEE. https://doi.org/10.1109/ITAB.2009.5394394

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Antoniou, P, Daykin, J, Iliopoulos, C, Kourie, D, Mouchard, L & Pissis, S 2009, Mapping uniquely occurring short sequences derived from high throughput technologies to a reference genome. in ITAB 2009: 9th International Conference on Information Technology and Applications in Biomedicine, 2009. N/A edn, vol. N/A, IEEE, Piscataway, N.J., pp. N/A. https://doi.org/10.1109/ITAB.2009.5394394

Mapping uniquely occurring short sequences derived from high throughput technologies to a reference genome. / Antoniou, P; Daykin, J; Iliopoulos, Costas et al.
ITAB 2009: 9th International Conference on Information Technology and Applications in Biomedicine, 2009. Vol. N/A N/A. ed. Piscataway, N.J.: IEEE, 2009. p. N/A.

Research output: Chapter in Book/Report/Conference proceeding › Conference paper

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

AU - Antoniou, P

AU - Daykin, J

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AU - Mouchard, L

AU - Pissis, Solon

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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.

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DO - 10.1109/ITAB.2009.5394394

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VL - N/A

SP - N/A

BT - ITAB 2009

PB - IEEE

CY - Piscataway, N.J.

ER -

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

Abstract

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