Bioinformatics: High Performance Parallel Computer Architectures (Hardcover)

Bertil Schmidt

  • 出版商: CRC
  • 出版日期: 2010-07-15
  • 定價: $5,980
  • 售價: 6.0$3,588
  • 語言: 英文
  • 頁數: 370
  • 裝訂: Hardcover
  • ISBN: 1439814880
  • ISBN-13: 9781439814888
  • 相關分類: 生物資訊 Bioinformatics
  • 立即出貨 (庫存=1)

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商品描述

New sequencing technologies have broken many experimental barriers to genome scale sequencing, leading to the extraction of huge quantities of sequence data. This expansion of biological databases established the need for new ways to harness and apply the astounding amount of available genomic information and convert it into substantive biological understanding.

A complilation of recent approaches from prominent researchers, Bioinformatics: High Performance Parallel Computer Architectures discusses how to take advantage of bioinformatics applications and algorithms on a variety of modern parallel architectures. Two factors continue to drive the increasing use of modern parallel computer architectures to address problems in computational biology and bioinformatics: high-throughput techniques for DNA sequencing and gene expression analysis—which have led to an exponential growth in the amount of digital biological data—and the multi- and many-core revolution within computer architecture.

Presenting key information about how to make optimal use of parallel architectures, this book:

  • Describes algorithms and tools including pairwise sequence alignment, multiple sequence alignment, BLAST, motif finding, pattern matching, sequence assembly, hidden Markov models, proteomics, and evolutionary tree reconstruction
  • Addresses GPGPU technology and the associated massively threaded CUDA programming model

  • Reviews FPGA architecture and programming
  • Presents several parallel algorithms for computing alignments on the Cell/BE architecture, including linear-space pairwise alignment, syntenic alignment, and spliced alignment
  • Assesses underlying concepts and advances in orchestrating the phylogenetic likelihood function on parallel computer architectures (ranging from FPGAs upto the IBM BlueGene/L supercomputer)
  • Covers several effective techniques to fully exploit the computing capability of many-core CUDA-enabled GPUs to accelerate protein sequence database searching, multiple sequence alignment, and motif finding
  • Explains a parallel CUDA-based method for correcting sequencing base-pair errors in HTSR data

Because the amount of publicly available sequence data is growing faster than single processor core performance speed, modern bioinformatics tools need to take advantage of parallel computer architectures. Now that the era of the many-core processor has begun, it is expected that future mainstream processors will be parallel systems. Beneficial to anyone actively involved in research and applications, this book helps you to get the most out of these tools and create optimal HPC solutions for bioinformatics.

商品描述(中文翻譯)

新的测序技术打破了许多基因组规模测序的实验障碍,导致大量的序列数据被提取出来。这种生物数据库的扩展建立了对新方法的需求,以利用和应用可用的大量基因组信息,并将其转化为实质性的生物学理解。

《生物信息学:高性能并行计算机架构》是一本由知名研究人员编写的最新方法的汇编,讨论了如何在各种现代并行架构上利用生物信息学应用和算法。两个因素继续推动现代并行计算机架构在计算生物学和生物信息学问题中的增加使用:高通量的DNA测序和基因表达分析技术,导致数字生物数据的指数增长,以及计算机架构中的多核和众核革命。

本书介绍了如何充分利用并行架构的关键信息,包括:

- 描述了算法和工具,包括成对序列比对、多序列比对、BLAST、模体发现、模式匹配、序列组装、隐藏马尔可夫模型、蛋白质组学和进化树重建。
- 讨论了GPGPU技术及其相关的大规模线程化CUDA编程模型。
- 回顾了FPGA架构和编程。
- 提出了在Cell/BE架构上计算比对的几种并行算法,包括线性空间成对比对、同源比对和剪接比对。
- 评估了在并行计算机架构上编排系统发育似然函数的基本概念和进展(从FPGA到IBM BlueGene/L超级计算机)。
- 讨论了几种有效的技术,充分利用众核CUDA可用的GPU来加速蛋白质序列数据库搜索、多序列比对和模体发现。
- 解释了一种基于CUDA的并行方法,用于纠正HTSR数据中的测序碱基错误。

由于公开可用的序列数据量增长速度超过了单处理器核心性能的速度,现代生物信息学工具需要利用并行计算机架构。现在,众核处理器时代已经开始,预计未来的主流处理器将是并行系统。对于任何积极参与研究和应用的人来说,本书将帮助您充分利用这些工具,并为生物信息学创建最佳的高性能计算解决方案。