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
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;
Conference_Titel :
Systems, Signals and Image Processing (IWSSIP), 2013 20th International Conference on
Conference_Location :
Bucharest
Print_ISBN :
978-1-4799-0941-4
DOI :
10.1109/IWSSIP.2013.6623487
