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 proceedingConference contributionAcademicpeer-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 languageEnglish
Title of host publicationProceedings of the Prague Stringology Conference 2009
Pages249-262
Number of pages14
Publication statusPublished - 1 Dec 2009
Externally publishedYes
EventPrague Stringology Conference 2009, PSC 2009 - Prague, Czech Republic
Duration: 31 Aug 20092 Sep 2009

Publication series

NameProceedings of the Prague Stringology Conference 2009

Conference

ConferencePrague Stringology Conference 2009, PSC 2009
Country/TerritoryCzech Republic
CityPrague
Period31/08/092/09/09

Keywords

  • High throughput sequencing tech- nologies
  • Parallel algorithms
  • String algorithms

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