benefit from an application-specific hardware architecture. References CLC bio and SciEngines collaborate on 188x acceleration of BLAST www.sciengines.com (Official site) www.copacobana.org Further reading Lars Wienbrandt, Bioinformatics Applications on the FPGA-based High-Performance Computer RIVYERA, in "High Performance Computing Using FPGAs" edited by Wim Vanderbauwhede, Khaled Benkrid, Springer, 2013, . Tim Güneysu, Timo Kasper, Martin Novotný, Christof Paar, Lars Wienbrandt, and Ralf Zimmermann, High-Performance Cryptanalysis on RIVYERA and COPACOBANA Computing Systems, in "High Performance Computing Using FPGAs" edited by Wim Vanderbauwhede, Khaled Benkrid, Springer, 2013, . Ayman Abbas, Claas Anders Rathje, Lars Wienbrandt, and Manfred Schimmler, Dictionary Attack on TrueCrypt with RIVYERA S3-5000, 2012 IEEE 18th International Conference on Parallel and Distributed Systems (ICPADS), Dec 2012, pp. 93–100. Florian Schatz, Lars Wienbrandt, and Manfred Schimmler, Probability model for boundaries of short-read sequencing, 2012 International Conference on Advances in Computing and Communications (ICACC), Aug 2012, pp. 223–228. (best paper award) Christoph Starke, Vasco Grossmann, Lars Wienbrandt, and Manfred Schimmler, An FPGA implementation of an Investment Strategy Processor, Procedia Computer Science, vol. 9, 2012, pp. 1880–1889. Lars Wienbrandt, Daniel Siebert, and Manfred Schimmler, Improvement of BLASTp on the FPGA-Based High-Performance Computer RIVYERA, Lecture Notes in Computer Science, vol. 7292, 2012, pp. 275–286. Christoph Starke, Vasco Grossmann, Lars Wienbrandt, Sven Koschnicke, John Carstens, and Manfred Schimmler, Optimizing Investment Strategies with the Reconfigurable Hardware Platform RIVYERA, International Journal of Reconfigurable Computing, vol. 2012, 10 pages. Lars Wienbrandt, Stefan Baumgart, Jost Bissel, Florian Schatz, and Manfred Schimmler, Massively parallel FPGA-based implementation of BLASTp with the two-hit method, Procedia Computer Science, vol. 4, 2011, pp. 1967–1976. Lars Wienbrandt, Hardware implementation and massive parallelization of BLAST, Invited talk: Workshop on Theoretical Biology, Max-Planck-Institute for Evolutionary Biology, Plön 2011. Lars Wienbrandt, and Manfred Schimmler, Collecting Statistical Information in DNA Sequences for the Detection of Special Motifs, Proceedings of BIOCOMP2010, 2010, pp. 274–278. Manfred Schimmler, Lars Wienbrandt, Tim Güneysu, and Jost Bissel, COPACOBANA: A Massively Parallel FPGA-Based Computer Architecture, in "Bioinformatics: High Performance Parallel Computer Architectures" edited by Bertil Schmidt, CRC Press, 2010, . Lars Wienbrandt, Stefan Baumgart, Jost Bissel, Carol May Yen Yeo, and Manfred Schimmler, Using the reconfigurable massively parallel architecture COPACOBANA 5000 for applications in bioinformatics, Procedia Computer Science, vol. 1 (1), 2010, pp. 1027–1034. Lars Wienbrandt, Massiv parallelisierte DNA-Motivsuche auf COPACOBANA - Hardware-Implementierung in VHDL und Effizienzvergleich mit einem Standard-PC, Diplomarbeit, Dezember 2008 Jan Schröder, Lars Wienbrandt, Gerd Pfeiffer, and Manfred Schimmler, Massively Parallelized DNA Motif Search