Coupling SIMD and SIMT architectures to boost performance of a phylogeny-aware alignment kernel

Coupling SIMD and SIMT architectures to boost performance of a phylogeny-aware alignment kernel

<p>Abstract</p> <p>Background</p> <p>Aligning short DNA reads to a reference sequence alignment is a prerequisite for detecting their biological origin and analyzing them in a phylogenetic context. With the PaPaRa tool we introduced a dedicated dynamic programming algor...

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Bibliographic Details
Main Authors: Alachiotis Nikolaos, Berger Simon A, Stamatakis Alexandros
Format: Article
Language:English
Published: BMC 2012-08-01
Series:BMC Bioinformatics
Subjects:
Alignment kernel
Dynamic programming
PaPaRa
OpenCL
SSE
SIMD
SIMT
GPU
Online Access:http://www.biomedcentral.com/1471-2105/13/196

Internet

http://www.biomedcentral.com/1471-2105/13/196

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