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Accelerated microRNA-Precursor Detection Using the Smith-Waterman Algorithm on FPGAs
May, Patrick; Klau, Gunnar W.; Bauer, Markus et al.
2007In Dubitzky, Werner; Schuster, Assaf; Sloot, Peterm A. et al. (Eds.) Distributed, High-Performance and Grid Computing in Computational Biology
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Keywords :
FPGA; microRNA; Smith-Waterman
Abstract :
[en] During the last few years more and more functionalities of RNA have been discovered that were previously thought of being carried out by proteins alone. One of the most striking discoveries was the detection of microRNAs, a class of noncoding RNAs that play an important role in post-transcriptional gene regulation. Large-scale analyses are needed for the still increasingly growing amount of sequence data derived from new experimental technologies. In this paper we present a framework for the detection of the distinctive precursor structure of microRNAS that is based on the well-known Smith-Waterman algorithm. By conducting the computation of the local alignment on a FPGA, we are able to gain a substantial speedup compared to a pure software implementation bringing together supercomputer performance and bioinformatics research. We conducted experiments on real genomic data and we found several new putative hits for microRNA precursor structures.
Disciplines :
Computer science
Author, co-author :
May, Patrick  ;  Zuse Insitute Berlin > Computer Science Research
Klau, Gunnar W.
Bauer, Markus
Steinke, Thomas
Language :
English
Title :
Accelerated microRNA-Precursor Detection Using the Smith-Waterman Algorithm on FPGAs
Publication date :
2007
Event name :
International Workshop, GCCB 2006
Event place :
Eilat, Israel
Event date :
January 21, 2007
Audience :
International
Main work title :
Distributed, High-Performance and Grid Computing in Computational Biology
Editor :
Dubitzky, Werner
Schuster, Assaf
Sloot, Peterm A.
Schroeder, Michael
Romberg, Mathilde
Publisher :
Springer Berlin Heidelberg, Berlin, Heidelberg, Germany
ISBN/EAN :
978-3-540-69841-8
Collection name :
Lecture Notes in Computer Science; 4360
Pages :
19-32
Peer reviewed :
Peer reviewed
Commentary :
4360
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since 23 April 2013

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