DocumentCode :
3495461
Title :
Workload optimization of proteomics pattern matching using embedded accelerator
Author :
Manole, Sagi ; Golander, Amit ; Weiss, Shlomo
Author_Institution :
Sch. of Electr. Eng., Tel Aviv Univ., Tel Aviv, Israel
fYear :
2010
fDate :
17-20 Nov. 2010
Abstract :
Digitalization has brought a tremendous momentum to the healthcare research. Recognition of patterns in one protein, which are similar to a functional site of another, is crucial for identifying possible functions of newly discovered proteins, as well as analysis of known proteins for previously undetermined activity. PROSITE is a comprehensive database which describes protein domains, families, functional sites and patterns to identify them. In this paper the workload is the task of locating patterns from the PROSITE database over proteins. We optimize the the workload by using IBM´s new Power Edge of Network processor (PowerEN) regular expression (RegX) hardware accelerator, which was built for deep-packet inspection at multiple 10Gbps ports. Our preliminary results demonstrate a speedup of 240 relative to software pattern matching. Moreover, indications show that speedup an order of magnitude higher is achievable.
Keywords :
health care; optimisation; pattern matching; proteins; proteomics; PROSITE database; comprehensive database; deep packet inspection; embedded accelerator; function identification; hardware accelerator; healthcare research; network processor; pattern location; pattern recognition; proteomic pattern matching; regular expression; software pattern matching; workload optimization; Amino acids; Databases; Engines; Hardware; Pattern matching; Proteins; Software;
fLanguage :
English
Publisher :
ieee
Conference_Titel :
Electrical and Electronics Engineers in Israel (IEEEI), 2010 IEEE 26th Convention of
Conference_Location :
Eliat
Print_ISBN :
978-1-4244-8681-6
Type :
conf
DOI :
10.1109/EEEI.2010.5662102
Filename :
5662102
Link To Document :
بازگشت