Reference : Accelerated microRNA-Precursor Detection Using the Smith-Waterman Algorithm on FPGAs
Scientific congresses, symposiums and conference proceedings : Paper published in a book
Engineering, computing & technology : Computer science
http://hdl.handle.net/10993/455
Accelerated microRNA-Precursor Detection Using the Smith-Waterman Algorithm on FPGAs
English
May, Patrick mailto [Zuse Insitute Berlin > Computer Science Research]
Klau, Gunnar W. [> >]
Bauer, Markus [> >]
Steinke, Thomas [> >]
2007
Distributed, High-Performance and Grid Computing in Computational Biology
Dubitzky, Werner
Schuster, Assaf
Sloot, Peterm A.
Schroeder, Michael
Romberg, Mathilde
Springer Berlin Heidelberg
Lecture Notes in Computer Science; 4360
19-32
Yes
No
International
978-3-540-69841-8
Berlin, Heidelberg
Germany
International Workshop, GCCB 2006
January 21, 2007
Eilat
Israel
[en] FPGA ; microRNA ; Smith-Waterman
[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.
Researchers ; Professionals
http://hdl.handle.net/10993/455
10.1007/978-3-540-69968-2_3
http://dx.doi.org/10.1007/978-3-540-69968-2_3
4360

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