DocumentCode
3397620
Title
Genome matching on modern architectures
Author
Lupescu, Grigore ; Pavaloiu, Bujor
Author_Institution
Fac. of Eng. in Foreign Languages, Univ. Politeh. of Bucharest, Bucharest, Romania
fYear
2013
fDate
7-9 July 2013
Firstpage
193
Lastpage
196
Abstract
Exact string matching algorithms are critical components in computational biology applications regarding the nucleotide or aminoacid sequences. The current paper presents a slightly modified version Boyer-Moore algorithm for string matching (in particular genomes) that has been optimized for a dual Xeon 5860. We highlight several ways to improve execution time and conclude based on our measurements that STTNI hardware instructions alongside core parallelism achieve most of the performance gain.
Keywords
DNA; biocomputing; organic compounds; pattern matching; software architecture; Boyer-Moore algorithm; STTNI hardware instructions; aminoacid sequences; computational biology applications; dual Xeon 5860; genome matching; modern architectures; nucleotide sequences; string matching algorithms; Bioinformatics; Genomics; Hardware; Multicore processing; Parallel processing; Program processors; DNA sequence; match; multicore; openmp; sse; string; sttni;
fLanguage
English
Publisher
ieee
Conference_Titel
Systems, Signals and Image Processing (IWSSIP), 2013 20th International Conference on
Conference_Location
Bucharest
ISSN
2157-8672
Print_ISBN
978-1-4799-0941-4
Type
conf
DOI
10.1109/IWSSIP.2013.6623487
Filename
6623487
Link To Document