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

Costas S. Iliopoulos; Mirka Miller; Solon P. Pissis

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

Costas S. Iliopoulos, Mirka Miller, Solon P. Pissis

Research output: Chapter in Book / Report / Conference proceeding › Conference contribution › Academic › peer-review

Abstract

Novel high throughput sequencing technologies have redefined the way genome sequencing is performed. They are able to produce millions of short sequences in a single experiment and with a much lower cost than previous methods. In this paper, we address the problem of efficiently mapping and classifying millions of de- generate and weighted sequences to a reference genome, based on whether they occur exactly once in the genome or not, and by taking into consideration probability scores. In particular, we design parallel algorithms for Massive Exact and Approximate Unique Pattern Matching for degenerate and weighted sequences derived from high throughput sequencing technologies.

Original language	English
Title of host publication	Proceedings of the Prague Stringology Conference 2009
Pages	249-262
Number of pages	14
Publication status	Published - 1 Dec 2009
Externally published	Yes
Event	Prague Stringology Conference 2009, PSC 2009 - Prague, Czech Republic Duration: 31 Aug 2009 → 2 Sept 2009

Publication series

Name	Proceedings of the Prague Stringology Conference 2009

Conference

Conference	Prague Stringology Conference 2009, PSC 2009
Country/Territory	Czech Republic
City	Prague
Period	31/08/09 → 2/09/09

Keywords

High throughput sequencing tech- nologies
Parallel algorithms
String algorithms

Persistent URL (handle)

Copy link address

Cite this

@inproceedings{2e795f1331d04fc198fa43fe6c7bab8a,

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

abstract = "Novel high throughput sequencing technologies have redefined the way genome sequencing is performed. They are able to produce millions of short sequences in a single experiment and with a much lower cost than previous methods. In this paper, we address the problem of efficiently mapping and classifying millions of de- generate and weighted sequences to a reference genome, based on whether they occur exactly once in the genome or not, and by taking into consideration probability scores. In particular, we design parallel algorithms for Massive Exact and Approximate Unique Pattern Matching for degenerate and weighted sequences derived from high throughput sequencing technologies.",

keywords = "High throughput sequencing tech- nologies, Parallel algorithms, String algorithms",

author = "Iliopoulos, {Costas S.} and Mirka Miller and Pissis, {Solon P.}",

year = "2009",

month = dec,

day = "1",

language = "English",

isbn = "9788001044032",

series = "Proceedings of the Prague Stringology Conference 2009",

pages = "249--262",

booktitle = "Proceedings of the Prague Stringology Conference 2009",

note = "Prague Stringology Conference 2009, PSC 2009 ; Conference date: 31-08-2009 Through 02-09-2009",

}

Parallel algorithms for degenerate and weighted sequences derived from high throughput sequencing technologies. / Iliopoulos, Costas S.; Miller, Mirka; Pissis, Solon P.
Proceedings of the Prague Stringology Conference 2009. 2009. p. 249-262 (Proceedings of the Prague Stringology Conference 2009).

Research output: Chapter in Book / Report / Conference proceeding › Conference contribution › Academic › peer-review

TY - GEN

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

AU - Iliopoulos, Costas S.

AU - Miller, Mirka

AU - Pissis, Solon P.

PY - 2009/12/1

Y1 - 2009/12/1

N2 - Novel high throughput sequencing technologies have redefined the way genome sequencing is performed. They are able to produce millions of short sequences in a single experiment and with a much lower cost than previous methods. In this paper, we address the problem of efficiently mapping and classifying millions of de- generate and weighted sequences to a reference genome, based on whether they occur exactly once in the genome or not, and by taking into consideration probability scores. In particular, we design parallel algorithms for Massive Exact and Approximate Unique Pattern Matching for degenerate and weighted sequences derived from high throughput sequencing technologies.

AB - Novel high throughput sequencing technologies have redefined the way genome sequencing is performed. They are able to produce millions of short sequences in a single experiment and with a much lower cost than previous methods. In this paper, we address the problem of efficiently mapping and classifying millions of de- generate and weighted sequences to a reference genome, based on whether they occur exactly once in the genome or not, and by taking into consideration probability scores. In particular, we design parallel algorithms for Massive Exact and Approximate Unique Pattern Matching for degenerate and weighted sequences derived from high throughput sequencing technologies.

KW - High throughput sequencing tech- nologies

KW - Parallel algorithms

KW - String algorithms

UR - http://www.scopus.com/inward/record.url?scp=79960094435&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=79960094435&partnerID=8YFLogxK

M3 - Conference contribution

AN - SCOPUS:79960094435

SN - 9788001044032

T3 - Proceedings of the Prague Stringology Conference 2009

SP - 249

EP - 262

BT - Proceedings of the Prague Stringology Conference 2009

T2 - Prague Stringology Conference 2009, PSC 2009

Y2 - 31 August 2009 through 2 September 2009

ER -

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

Abstract

Publication series

Conference

Keywords

Persistent URL (handle)

Other files and links

Fingerprint

Cite this