GapMis-OMP: Pairwise short-read alignment on multi-core architectures

Tomáš Flouri*, Costas S. Iliopoulos, Kunsoo Park, Solon P. Pissis

*Corresponding author for this work

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

Abstract

Pairwise sequence alignment has received a new motivation due to the advent of next-generation sequencing technologies, particularly so for the application of re-sequencing-the assembly of a genome directed by a reference sequence. After the fast alignment between a factor of the reference sequence and a high-quality fragment of a short read by a short-read alignment programme, an important problem is to find the alignment between a relatively short succeeding factor of the reference sequence and the remaining low-quality fragment of the read allowing a number of mismatches and the insertion of a single gap in the alignment. In this article, we present GapMis-OMP, a tool for pairwise short-read alignment that works on multi-core architectures. It is designed to compute the alignments between all the sequences in a first set of sequences and all those from a second one in parallel. The presented experimental results demonstrate that GapMis-OMP is more efficient than most popular tools.

Original languageEnglish
Title of host publicationArtificial Intelligence Applications and Innovations - AIAI 2012 International Workshops
Subtitle of host publicationAIAB, AIeIA, CISE, COPA, IIVC, ISQL, MHDW, and WADTMB, Proceedings
PublisherSpringer New York LLC
Pages593-601
Number of pages9
EditionPART 2
ISBN (Print)9783642334115
DOIs
Publication statusPublished - 1 Jan 2012
Externally publishedYes
Event8th International Workshop on Artificial Intelligence Applications and Innovations, AIAI 2012: AIAB, AIeIA, CISE, COPA, IIVC, ISQL, MHDW, and WADTMB - Halkidiki, Greece
Duration: 27 Sept 201230 Sept 2012

Publication series

NameIFIP Advances in Information and Communication Technology
NumberPART 2
Volume382 AICT
ISSN (Print)1868-4238

Conference

Conference8th International Workshop on Artificial Intelligence Applications and Innovations, AIAI 2012: AIAB, AIeIA, CISE, COPA, IIVC, ISQL, MHDW, and WADTMB
Country/TerritoryGreece
CityHalkidiki
Period27/09/1230/09/12

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