Accelerated microRNA-Precursor Detection Using the Smith-Waterman Algorithm on FPGAs

  • Patrick May
  • Gunnar W. Klau
  • Markus Bauer
  • Thomas Steinke
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 4360)


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.


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Copyright information

© Springer Berlin Heidelberg 2007

Authors and Affiliations

  • Patrick May
    • 1
    • 2
  • Gunnar W. Klau
    • 3
    • 4
  • Markus Bauer
    • 1
    • 5
  • Thomas Steinke
    • 2
  1. 1.Algorithmic Bioinformatics, Institute of Computer Science, Free University BerlinGermany
  2. 2.Computer Science Research, Zuse Institute BerlinGermany
  3. 3.Mathematics in Life Sciences, Institute of Mathematics, Free University BerlinGermany
  4. 4.DFG Research Center Matheon “Mathematics for key technologies”, BerlinGermany
  5. 5.International Max Planck Research School for Computational Biology, and Scientific Computing, BerlinGermany

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