Practical and efficient algorithms for degenerate and weighted sequences derived from high throughput sequencing technologies

Pavlos Antoniou; Costas S. Iliopoulos; Laurent Mouchard; Solon Pissis

doi:10.1109/IJCBS.2009.48

Practical and efficient algorithms for degenerate and weighted sequences derived from high throughput sequencing technologies

Pavlos Antoniou, Costas S. Iliopoulos, Laurent Mouchard, Solon Pissis

Informatics

King's College London

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

1 Citation (Scopus)

Abstract

High throughput, (or next generation) sequencing technologies have opened new and exciting opportunities in the use of DNA sequences. The new emerging technologies mark the beginning of a new era of high throughput short read sequencing: they have the potential to assemble a bacterial genome during a single experiment and at a moderate cost. In this paper we address the problem of efficiently mapping millions of degenerate and weighted sequences to a reference genome with respect to whether they occur exactly once in the genome or not, and by taking probability scores into consideration In particular we define and solve the Massive Exact and Approximate Unique Pattern Matching problem for degenerate and weighted sequences derived from high throughput sequencing technologies.

Original language	English
Title of host publication	IJCBS 2009
Subtitle of host publication	International Joint Conference on Bioinformatics, Systems Biology and Intelligent Computing, 2009
Editors	Joe Zhang, Guozheng Li, Y Jack
Place of Publication	Los Alamitos
Publisher	IEEE Computer Society
Pages	174-180
Number of pages	7
Volume	N/A
Edition	N/A
ISBN (Print)	9780769537399
DOIs	https://doi.org/10.1109/IJCBS.2009.48
Publication status	Published - 2009
Event	International Joint Conference on Bioinformatics, Systems Biology and Intelligent Computing - Shanghai, China Duration: 3 Aug 2009 → 5 Aug 2009

Conference

Conference	International Joint Conference on Bioinformatics, Systems Biology and Intelligent Computing
Country/Territory	China
City	Shanghai
Period	3/08/2009 → 5/08/2009

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10.1109/IJCBS.2009.48

Cite this

Antoniou, P., Iliopoulos, C. S., Mouchard, L., & Pissis, S. (2009). Practical and efficient algorithms for degenerate and weighted sequences derived from high throughput sequencing technologies. In J. Zhang, G. Li, & Y. Jack (Eds.), IJCBS 2009: International Joint Conference on Bioinformatics, Systems Biology and Intelligent Computing, 2009 (N/A ed., Vol. N/A, pp. 174-180). IEEE Computer Society. https://doi.org/10.1109/IJCBS.2009.48

Antoniou, Pavlos ; Iliopoulos, Costas S. ; Mouchard, Laurent et al. / Practical and efficient algorithms for degenerate and weighted sequences derived from high throughput sequencing technologies. IJCBS 2009: International Joint Conference on Bioinformatics, Systems Biology and Intelligent Computing, 2009. editor / Joe Zhang ; Guozheng Li ; Y Jack. Vol. N/A N/A. ed. Los Alamitos : IEEE Computer Society, 2009. pp. 174-180

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title = "Practical and efficient algorithms for degenerate and weighted sequences derived from high throughput sequencing technologies",

abstract = "High throughput, (or next generation) sequencing technologies have opened new and exciting opportunities in the use of DNA sequences. The new emerging technologies mark the beginning of a new era of high throughput short read sequencing: they have the potential to assemble a bacterial genome during a single experiment and at a moderate cost. In this paper we address the problem of efficiently mapping millions of degenerate and weighted sequences to a reference genome with respect to whether they occur exactly once in the genome or not, and by taking probability scores into consideration In particular we define and solve the Massive Exact and Approximate Unique Pattern Matching problem for degenerate and weighted sequences derived from high throughput sequencing technologies.",

author = "Pavlos Antoniou and Iliopoulos, {Costas S.} and Laurent Mouchard and Solon Pissis",

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doi = "10.1109/IJCBS.2009.48",

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volume = "N/A",

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editor = "Joe Zhang and Guozheng Li and Y Jack",

booktitle = "IJCBS 2009",

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note = "International Joint Conference on Bioinformatics, Systems Biology and Intelligent Computing ; Conference date: 03-08-2009 Through 05-08-2009",

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Antoniou, P, Iliopoulos, CS , Mouchard, L & Pissis, S 2009, Practical and efficient algorithms for degenerate and weighted sequences derived from high throughput sequencing technologies. in J Zhang, G Li & Y Jack (eds), IJCBS 2009: International Joint Conference on Bioinformatics, Systems Biology and Intelligent Computing, 2009. N/A edn, vol. N/A, IEEE Computer Society, Los Alamitos, pp. 174-180, International Joint Conference on Bioinformatics, Systems Biology and Intelligent Computing, Shanghai, China, 3/08/2009. https://doi.org/10.1109/IJCBS.2009.48

Practical and efficient algorithms for degenerate and weighted sequences derived from high throughput sequencing technologies. / Antoniou, Pavlos; Iliopoulos, Costas S.; Mouchard, Laurent et al.
IJCBS 2009: International Joint Conference on Bioinformatics, Systems Biology and Intelligent Computing, 2009. ed. / Joe Zhang; Guozheng Li; Y Jack. Vol. N/A N/A. ed. Los Alamitos: IEEE Computer Society, 2009. p. 174-180.

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

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T1 - Practical and efficient algorithms for degenerate and weighted sequences derived from high throughput sequencing technologies

AU - Antoniou, Pavlos

AU - Iliopoulos, Costas S.

AU - Mouchard, Laurent

AU - Pissis, Solon

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N2 - High throughput, (or next generation) sequencing technologies have opened new and exciting opportunities in the use of DNA sequences. The new emerging technologies mark the beginning of a new era of high throughput short read sequencing: they have the potential to assemble a bacterial genome during a single experiment and at a moderate cost. In this paper we address the problem of efficiently mapping millions of degenerate and weighted sequences to a reference genome with respect to whether they occur exactly once in the genome or not, and by taking probability scores into consideration In particular we define and solve the Massive Exact and Approximate Unique Pattern Matching problem for degenerate and weighted sequences derived from high throughput sequencing technologies.

AB - High throughput, (or next generation) sequencing technologies have opened new and exciting opportunities in the use of DNA sequences. The new emerging technologies mark the beginning of a new era of high throughput short read sequencing: they have the potential to assemble a bacterial genome during a single experiment and at a moderate cost. In this paper we address the problem of efficiently mapping millions of degenerate and weighted sequences to a reference genome with respect to whether they occur exactly once in the genome or not, and by taking probability scores into consideration In particular we define and solve the Massive Exact and Approximate Unique Pattern Matching problem for degenerate and weighted sequences derived from high throughput sequencing technologies.

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DO - 10.1109/IJCBS.2009.48

M3 - Conference paper

SN - 9780769537399

VL - N/A

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EP - 180

BT - IJCBS 2009

A2 - Zhang, Joe

A2 - Li, Guozheng

A2 - Jack, Y

PB - IEEE Computer Society

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T2 - International Joint Conference on Bioinformatics, Systems Biology and Intelligent Computing

Y2 - 3 August 2009 through 5 August 2009

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Antoniou P, Iliopoulos CS , Mouchard L , Pissis S. Practical and efficient algorithms for degenerate and weighted sequences derived from high throughput sequencing technologies. In Zhang J, Li G, Jack Y, editors, IJCBS 2009: International Joint Conference on Bioinformatics, Systems Biology and Intelligent Computing, 2009. N/A ed. Vol. N/A. Los Alamitos: IEEE Computer Society. 2009. p. 174-180 doi: 10.1109/IJCBS.2009.48

Practical and efficient algorithms for degenerate and weighted sequences derived from high throughput sequencing technologies

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