Protein Sequence Pattern Matching: Leveraging Application Specific Hardware Accelerators

Digitalization has brought a tremendous momentum to health care research. Recognition of patterns in proteins is crucial for identifying possible functions of newly discovered proteins, as well as analysis of known proteins for previously undetermined activity. In this paper, the workload consists o...

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Bibliographic Details
Published inIEEE transactions on computers Vol. 63; no. 2; pp. 448 - 460
Main Authors Manole, Sagi, Golander, Amit, Weiss, Shlomo
Format Journal Article
LanguageEnglish
Published IEEE 01.02.2014
Subjects
CMP
Hardware
hardware accelerator
Instruction sets
Multithreading
Pattern matching
Processor scheduling
Protein sequence
Proteins
SMT
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Summary:Digitalization has brought a tremendous momentum to health care research. Recognition of patterns in proteins is crucial for identifying possible functions of newly discovered proteins, as well as analysis of known proteins for previously undetermined activity. In this paper, the workload consists of locating patterns from the PROSITE database in protein sequences. We optimize the pattern search task by using a new breed of processors that merge network and server attributes. We leverage massive multithreading and regular-expression (RegX) hardware accelerators; the latter were designed and built for an entirely different application - high-bandwidth deep-packet inspection. Our multithreading optimization achieves 18x improvement, but by harnessing a RegX accelerator we were able to further demonstrate a significant 392x improvement relative to software pattern matching. Moreover, performance per area and power consumption are improved by multiple orders of magnitude as well.
ISSN:0018-9340
1557-9956
DOI:10.1109/TC.2012.187