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

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

*Corresponding author for this work

Research output: Chapter in Book / Report / Conference proceedingConference contributionAcademicpeer-review

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 languageEnglish
Title of host publicationProceedings - 2009 International Joint Conference on Bioinformatics, Systems Biology and Intelligent Computing, IJCBS 2009
Pages174-180
Number of pages7
DOIs
Publication statusPublished - 26 Nov 2009
Externally publishedYes
Event2009 International Joint Conference on Bioinformatics, Systems Biology and Intelligent Computing, IJCBS 2009 - Shanghai, China
Duration: 3 Aug 20095 Aug 2009

Publication series

NameProceedings - 2009 International Joint Conference on Bioinformatics, Systems Biology and Intelligent Computing, IJCBS 2009

Conference

Conference2009 International Joint Conference on Bioinformatics, Systems Biology and Intelligent Computing, IJCBS 2009
Country/TerritoryChina
CityShanghai
Period3/08/095/08/09

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