کد مقاله کد نشریه سال انتشار مقاله انگلیسی نسخه تمام متن
461701 696624 2009 9 صفحه PDF دانلود رایگان
عنوان انگلیسی مقاله ISI
Acceleration of ungapped extension in Mercury BLAST
موضوعات مرتبط
مهندسی و علوم پایه مهندسی کامپیوتر شبکه های کامپیوتری و ارتباطات
پیش نمایش صفحه اول مقاله
Acceleration of ungapped extension in Mercury BLAST
چکیده انگلیسی

The amount of biosequence data being produced each year is growing exponentially. Extracting useful information from this massive amount of data efficiently is becoming an increasingly difficult task. There are many available software tools that molecular biologists use for comparing genomic data. This paper focuses on accelerating the most widely used such tool, BLAST. Mercury BLAST takes a streaming approach to the BLAST computation by offloading the performance-critical sections to specialized hardware. This hardware is then used in combination with the processor of the host system to deliver BLAST results in a fraction of the time of the general-purpose processor alone.This paper presents the design of the ungapped extension stage of Mercury BLAST. The architecture of the ungapped extension stage is described along with the context of this stage within the Mercury BLAST system. The design is compact and runs at 100 MHz on available FPGAs, making it an effective and powerful component for accelerating biosequence comparisons. The performance of this stage is 25× that of the standard software distribution, yielding close to 50× performance improvement on the complete BLAST application. The sensitivity is essentially equivalent to that of the standard distribution.

ناشر
Database: Elsevier - ScienceDirect (ساینس دایرکت)
Journal: Microprocessors and Microsystems - Volume 33, Issue 4, June 2009, Pages 281–289
نویسندگان
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