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Graphics card processing : accelerating profile-profile alignment
Citation Link: https://doi.org/10.15480/882.2302
Publikationstyp
Journal Article
Date Issued
2012
Sprache
English
Author(s)
Institut
TORE-DOI
TORE-URI
Journal
Volume
2
Issue
4
Start Page
367
End Page
388
Citation
Central European journal of computer science 4 (2): 367-388 (2012)
Publisher DOI
Scopus ID
Publisher
De Gruyter
© 2012 Versita Warsaw. Alignment is the fundamental operation in molecular biology for comparing biomolecular sequences. The most widely used method for aligning groups of alignments is based on the alignment of the profiles corresponding to the groups. We show that profile-profile alignment can be significantly speeded up by general purpose computing on a modern commodity graphics card. Wavefront and matrix-matrix product approaches for implementing profile-profile alignment onto graphics processor are analyzed. The average speed-up obtained is one order of magnitude even when overheads are considered. Thus the computational power of graphics cards can be exploited to develop improved solutions for multiple sequence alignment.
Subjects
alignment
progressive alignment
graphics processor card
basic linear algebra subprograms
performance
DDC Class
510: Mathematik
600: Technik
620: Ingenieurwissenschaften
More Funding Information
DAAD, Deutscher Akademischer Austausch-Dienst; Higher Education Commission of Pakistan
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[Open Computer Science] Graphics card processing accelerating profile-profile alignment.pdf
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