Biosequence similarity search is an important application in modern molecular biology. Search algorithms aim to identify sets of sequences whose extensional similarity suggests a common evolutionary origin or function. The most widely used similarity search tool for biosequences is BLAST, a program designed to compare query sequences to a database. Here, we present the design of BLASTN, the version of BLAST that searches DNA sequences, on the Mercury system, an architecture that supports high-volume, high-throughput data movement off a data store and into reconfigurable hardware. An important component of application deployment on the Mercury system is the functional decomposition of the application onto both the reconfigurable hardware and the traditional processor. Both the Mercury BLASTN application design and its performance analysis are described.

中文翻译：

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汞系统上的生物序列相似性搜索。

生物序列相似性搜索是现代分子生物学中的重要应用。搜索算法旨在识别其延伸相似性暗示共同进化起源或功能的序列集。用于生物序列的最广泛使用的相似性搜索工具是BLAST，该程序旨在将查询序列与数据库进行比较。在这里，我们介绍Mercury系统上BLASTN的设计，BLASTN是搜索DNA序列的BLAST版本，该体系结构支持从数据存储到可重配置硬件的高容量，高吞吐量数据移动。Mercury系统上应用程序部署的重要组成部分是将应用程序功能分解到可重新配置的硬件和传统处理器上。