Fast Biosequence Annotation via Reconfigurable Hardware

描述(由申请人提供)：生物序列数据库已被证明对了解人类和其他基因组的组织、揭开遗传疾病的病因学以及研究医学上重要的病原体有价值。不幸的是，这些数据库正在以指数级的速度增长，这给生物序列标注带来了严重的问题。序列比较的专用硬件实现可以极大地加速BLAST和用于注释序列的其他算法。然而，这些硬件加速器的用途受到以下因素的限制：不灵活的功能、缺乏到更快组件的明确升级路径、以及生物序列数据可以被流到比较逻辑的速率的限制。这一提议旨在构建一种新型的基于硬件的生物序列加速器，即解决现有加速器局限性的智能磁盘引擎。该引擎结合了可重新配置的FPGA逻辑的灵活性，可以随意重新编程，在以硬件速度运行时很容易升级，以及将比较逻辑紧密绑定到硬盘阵列的创新架构，保证了比较硬件的海量数据带宽。智能磁盘引擎旨在加速BLAST式相似性搜索算法的所有阶段，而不仅仅是最后的史密斯-沃特曼阶段。这一快速跟踪STTR应用的第一阶段建议构建智能磁盘引擎的初始原型，实现对广泛使用的BLAST流水线的阶段的比较逻辑镜像，构建对引擎透明的软件前端，最后评估原型在生物序列标注中的大规模任务上的性能。这一阶段的关键创新将是将现场可编程门阵列逻辑与大容量存储系统集成，对新体系结构的性能进行建模，以及开发可以快速对现场可编程门阵列进行重新编程的软件控制，以构建针对不同类型的比较(BLASTN、BLASTP等)进行优化的比较流水线。在这一阶段结束时，智能磁盘原型的硬件和软件组合应该至少执行类似BLASTN和BLASTP的计算，运行速度至少比2003年代的商用通用处理器快30倍，并成功地向生物最终用户隐藏了引擎硬件的复杂性。

DESCRIPTION (provided by applicant): Databases of biological sequences have proven valuable for understanding the organization of human and other genomes, for unraveling the etiology of genetic disorders, and for studying medically important pathogens. Unfortunately, these databases are growing at an exponential rate, posing a severe problem for bio-sequence annotation. Specialized hardware implementations of sequence comparison can dramatically accelerate BLAST and other algorithms used to annotate sequences. However, the utility of these hardware accelerators is limited by inflexible functionality, lack of a clear upgrade path to faster components, and limitations on the rate at which bio-sequence data can be streamed to the comparison logic. This proposal seeks to construct a novel hardware-based bio-sequence accelerator, the "smart disk" engine that addresses limitations of existing accelerators. The proposed engine combines the flexibility of reconfigurable FPGA logic, which can be reprogrammed at will and easily upgraded while running at hardware speeds, with an innovative architecture that ties the comparison logic closely to an array of hard disks, guaranteeing massive data bandwidth into the comparison hardware. The smart disk engine is designed to accelerate all stages of BLAST-like similarity search algorithms, not just the final Smith- Waterman stage. Phase I of this fast-track STTR application proposes to build the initial prototype of the smart disk engine, to implement comparison logic mirroring the stages of the widely used BLAST pipeline, to construct a transparent software front end to the engine, and finally to evaluate the performance of the prototype on large-scale tasks in bio-sequence annotation. Key innovations in this phase will be the integration of FPGA logic with the mass storage system, modeling the performance of the new architecture, and development of software control that can rapidly reprogram the FPGAs to construct comparison pipelines optimized for different types of comparison (BLASTN, BLASTP, etc). At the end of this phase, the combined hardware and software of the smart disk prototype should implement at least BLASTN- and BLASTP-like computations, run at least 30x faster than 2003-era commodity general-purpose processors, and successfully hide the complexity of the engine's hardware from the biological end user.