TY - CHAP
T1 - A parallel GPU-designed algorithm for the constrained multiple sequence alignment problem
AU - Gudyś, Adam
AU - Deorowicz, Sebastian
PY - 2011
Y1 - 2011
N2 - Modern graphical processing units (GPUs) offer much more computational power than modern CPUs, so it is natural that GPUs are often used for solving many computationally-intensive problems. One of the tasks of huge importance in bioinformatics is sequence alignment. We investigate its variant introduced a few years ago in which some additional requirement on the alignment is given. As a result we propose a parallel version of Center-Star algorithm computing the constrained multiple sequence alignment at the GPU. The obtained speedup over the serial CPU relative is in range [20, 200].
AB - Modern graphical processing units (GPUs) offer much more computational power than modern CPUs, so it is natural that GPUs are often used for solving many computationally-intensive problems. One of the tasks of huge importance in bioinformatics is sequence alignment. We investigate its variant introduced a few years ago in which some additional requirement on the alignment is given. As a result we propose a parallel version of Center-Star algorithm computing the constrained multiple sequence alignment at the GPU. The obtained speedup over the serial CPU relative is in range [20, 200].
KW - GPU General Processing
KW - constrained sequence alignment
UR - https://www.scopus.com/pages/publications/80052927525
U2 - 10.1007/978-3-642-23169-8_39
DO - 10.1007/978-3-642-23169-8_39
M3 - Chapter
AN - SCOPUS:80052927525
SN - 9783642231681
T3 - Advances in Intelligent and Soft Computing
SP - 361
EP - 368
BT - Man-Machine Interactions 2
A2 - Czachorski, Tadeusz
A2 - Kozielski, Stanislaw
A2 - Stanczyk, Urszula
ER -