Electrical Engineering-Systems Dept.

*** SEMINAR ***

Sagi Manole

(M.Sc. student under the supervision of Prof' Shlomo Weiss)

On the subject:

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 of locating patterns from the PROSITE database in protein sequences. The pattern search task is optimized by using a new breed of processors that merge network and server attributes. Additionally, massive multithreading and Regular-Expression (RegX ) hardware accelerators are leveraged; the latter were designed and built for an entirely different application -- high-bandwidth deep-packet inspection. The multithreading optimization technique used in this research achieves 18x improvement, but by harnessing a RegX accelerator a signi_cant 392x improvement is demonstrated relative to software pattern matching. Moreover, performance per area and power consumption are improved by multiple orders of magnitude as well.