An algorithm for mapping short reads to a dynamically changing genomic sequence

Tomáš Flouri*, Jan Holub, Costas S. Iliopoulos, Solon Pissis

*Corresponding author for this work

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

Abstract

The constant advances in sequencing technology have redefined the way genome sequencing is performed. They are able to produce tens of millions of short sequences (reads), during a single experiment, and with a much lower cost than previously possible. Due to this massive amount of data, efficient algorithms for mapping these reads to reference sequences are in great demand, and recently, there has been ample work for publishing such algorithms. In this paper, we study a different version of this problem: mapping these reads to a dynamically changing genomic sequence. We propose a new practical algorithm, which employs a suitable data structure that takes into account potential dynamic effects (replacements, insertions, deletions) on the genomic sequence. The presented experimental results demonstrate that the proposed approach can be applied to address the problem of mapping millions of reads to multiple genomic sequences.

Original languageEnglish
Title of host publicationProceedings - 2010 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2010
Pages133-136
Number of pages4
DOIs
Publication statusPublished - 1 Dec 2010
Externally publishedYes
Event2010 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2010 - Hong Kong, China
Duration: 18 Dec 201021 Dec 2010

Publication series

NameProceedings - 2010 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2010

Conference

Conference2010 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2010
CountryChina
CityHong Kong
Period18/12/1021/12/10

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