| [176909] |
| Title: Graphics card processing: accelerating profile-profile alignment. |
| Written by: Muhammad Kashif Hanif and Karl-Heinz Zimmermann |
| in: <em>Central European Journal of Computer Science (CEJCS)</em>. December (2012). |
| Volume: <strong>2</strong>. Number: (4), |
| on pages: 367-388 |
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| Publisher: De Gruyter Open: |
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| ISBN: 10.2478/s13537-012-0033-5 |
| how published: 12-03 HaZi12 CEJCS |
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Note: khzimmermann, AEG
Abstract: 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.