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Architecture Exploration of FPGA Based Accelerators for BioInformatics Applications

  • B. Sharat Chandra Varma
  • Kolin Paul
  • M. Balakrishnan

Part of the Springer Series in Advanced Microelectronics book series (MICROELECTR., volume 55)

Table of contents

  1. Front Matter
    Pages i-xv
  2. B. Sharat Chandra Varma, Kolin Paul, M. Balakrishnan
    Pages 1-8
  3. B. Sharat Chandra Varma, Kolin Paul, M. Balakrishnan
    Pages 9-28
  4. B. Sharat Chandra Varma, Kolin Paul, M. Balakrishnan
    Pages 29-38
  5. B. Sharat Chandra Varma, Kolin Paul, M. Balakrishnan
    Pages 39-54
  6. B. Sharat Chandra Varma, Kolin Paul, M. Balakrishnan
    Pages 55-79
  7. B. Sharat Chandra Varma, Kolin Paul, M. Balakrishnan
    Pages 81-99
  8. B. Sharat Chandra Varma, Kolin Paul, M. Balakrishnan
    Pages 101-116
  9. B. Sharat Chandra Varma, Kolin Paul, M. Balakrishnan
    Pages 117-120
  10. Back Matter
    Pages 121-122

About this book

Introduction

This book presents an evaluation methodology to design future FPGA fabrics incorporating hard embedded blocks (HEBs) to accelerate applications. This methodology will be useful for selection of blocks to be embedded into the fabric and for evaluating the performance gain that can be achieved by such an embedding. The authors illustrate the use of their methodology by studying the impact of HEBs on two important bioinformatics applications: protein docking and genome assembly. The book also explains how the respective HEBs are designed and how hardware implementation of the application is done using these HEBs. It shows that significant speedups can be achieved over pure software implementations by using such FPGA-based accelerators. The methodology presented in this book may also be used for designing HEBs for accelerating software implementations in other domains besides bioinformatics. This book will prove useful to students, researchers, and practicing engineers alike.

Keywords

BioInformatics FPGA FPGA Accelerators HEB design Hard embedded blocks Velvet de novo

Authors and affiliations

  • B. Sharat Chandra Varma
    • 1
  • Kolin Paul
    • 2
  • M. Balakrishnan
    • 3
  1. 1.Elect&Elctro Engg,Chow Yei Ching BldgThe University of Hong KongHong KongHong Kong
  2. 2.Computer Science & EngineeringIndian Institute of Technology DelhiDelhiIndia
  3. 3.Computer Science and EngineeringIndian Institute of Technology DelhiNew DelhiIndia

Bibliographic information

  • DOI https://doi.org/10.1007/978-981-10-0591-6
  • Copyright Information Springer Science+Business Media Singapore 2016
  • Publisher Name Springer, Singapore
  • eBook Packages Engineering
  • Print ISBN 978-981-10-0589-3
  • Online ISBN 978-981-10-0591-6
  • Series Print ISSN 1437-0387
  • Series Online ISSN 2197-6643
  • Buy this book on publisher's site
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