Bioinformatics : high performance parallel computer architectures / edited by Bertil Schmidt. — Boca Raton, Fla. : CRC, c2011. – (58.17115/B615h)

Contents

    Contents
    
    Preface
    Editor
    Contributors
    1. Algorithms for Bioinformatics 1
    2. Introduction to GPGPUs and Massively Threaded Programming 29
    3. FPGA: Architecture and Programming 49
    4. Parallel Algorithms for Alignments on the Cell BE 59
    5. Orchestrating the Phylogenetic Likelihood Function on Emerging Parallel Architectures 85
    6. Parallel Bioinformatics Algorithms for CUDA-Enabled GPUs 117
    7. CUDA Error Correction Method for High-Throughput Short-Read Sequencing Data 139
    8. FPGA Acceleration of Seeded Similarity Searching 157
    9. Seed-Based Parallel Protein Sequence Comparison Combining Multithreading， GPU， and FPGA Technologies 181
    10. Database Searching with Profile-Hidden Markov Models on Reconfigurable and Many-Core Architectures 203
    11. COPACOBANA: A Massively Parallel FPGA-Based Computer Architecture 223
    12. Accelerating String Set Matching for Bioinformatics Using FPGA Hardware 263
    13. Reconfigurable Neural System and Its Application to Dimeric Protein Binding Site Identification 285
    14. Parallel FPGA Search Engine for Protein Identification 313
    Index 337