Bioinformatics: high performance parallel computer architectures / ed. by B.Schmidt. - Boca Raton: CRC, 2011. - xiv, 356 p.: ill. - (Embedded multi-core systems). - Incl. bibl. ref. - Ind.: p.337-356. - ISBN 978-1-4398-1498-8  Место хранения:   03 | Центральная библиотека Иркутского научного центра СО РАН | Иркутск

Оглавление / Contents

Preface ....................................................... vii Editor ......................................................... xi Contributors ................................................. xiii 1 Algorithms for Bioinformatics ................................ 1 Bertil Schmidt 2 Introduction to GPGPUs and Massively Threaded Programming ... 29 Robert M. Farber 3 FPGA: Architecture and Programming .......................... 49 Douglas Maskell 4 Parallel Algorithms for Alignments on the Cell BE ........... 59 Abhinav Sarje and Srinivas Aluru 5 Orchestrating the Phylogenetic Likelihood Function on Emerging Parallel Architectures ............................. 85 Alexandros Stamatakis 6 Parallel Bioinformatics Algorithms for CUDA-Enabled GPUs ... 117 Yongchao Liu, Bertil Schmidt, and Douglas Maskell 7 CUDA Error Correction Method for High-Throughput Short- Read Sequencing Data ....................................... 139 Haixiang Shi, Weiguo Liu, and Bertil Schmidt 8 FPGA Acceleration of Seeded Similarity Searching ........... 157 Arpith C. Jacob, Joseph M. Lancaster, Jeremy D. Buhler, and Roger D. Chamberlain 9 Seed-Based Parallel Protein Sequence Comparison Combining Multithreading, GPU, and FPGA Technologies ................. 181 Dominique Lavenier and Van-Hoa Nguyen 10 Database Searching with Profile-Hidden Markov Models on Reconfigurable and Many-Core Architectures ................. 203 John Paul Walters, Vipin Chaudhary, and Bertil Schmidt 11 COPACOBANA: A Massively Parallel FPGA-Based Computer Architecture ............................................... 223 Manfred Schimmler, Lars Wienbrandt, Tim Güneysu, and Jost Bissel 12 Accelerating String Set Matching for Bioinformatics Using FPGA Hardware .............................................. 263 Yoginder S. Dandass 13 Reconfigurable Neural System and Its Application to Dimeric Protein Binding Site Identification ................ 285 Feng Lin and Maria Stepanova 14 Parallel FPGA Search Engine for Protein Identification ..... 313 Daniel Coca, Istvan Bogdan, and Robert J. Beynon Index ......................................................... 337