Title :
An Optimized System for Multiple Sequence Alignment
Author :
Ylmaz, C. ; Gok, M.
Author_Institution :
Dept. of Comput. Eng., Cukurova Univ., Balcali, Turkey
Abstract :
Multiple sequence alignment (MSA) is one of the essential operations for identifying functional and structural relations among proteins. The execution of an MSA algorithm requires high-performance platforms. This paper presents a hardware system that speeds up the popular MSA software ClustalW. The proposed design performs the computation of the most time consuming step of the ClustalW. Test results show that the proposed hardware increases the performance of this step up to 85 times.
Keywords :
biology computing; field programmable gate arrays; molecular biophysics; molecular configurations; optimisation; proteins; FPGA implementations; MSA software ClustalW; functional-structural relation; hardware system; multiple sequence alignment; optimized system; proteins; Algorithm design and analysis; Design methodology; Engines; Field programmable gate arrays; Hardware; Heuristic algorithms; Phylogeny; Protein engineering; Sequences; System testing; ClustalW; Hardware; Multiple Sequence Alignment;
Conference_Titel :
Reconfigurable Computing and FPGAs, 2009. ReConFig '09. International Conference on
Conference_Location :
Quintana Roo
Print_ISBN :
978-1-4244-5293-4
DOI :
10.1109/ReConFig.2009.82
