Skip to Main Content
 

Global Search Box

 
 
 
 

Files

File List


ThesisSubmit.pdf (695.71 KB)

ETD Abstract Container

Abstract Header

A PAIRWISE COMPARISON OF DNA SEQUENCE ALIGNMENT USING AN OPENMP IMPLEMENTATION OF THE SWAMP PARALLEL SMITH-WATERMAN ALGORITHM

Cuevas, Tristan Lee
http://orcid.org/0000-0003-1175-4556
http://rave.ohiolink.edu/etdc/view?acc_num=kent1429528937

Abstract Details

2015, MS, Kent State University, College of Arts and Sciences / Department of Computer Science.
This research develops an OpenMP solution for a pairwise comparison of DNA sequence data strings using an extended Smith-Waterman algorithm. The CSX600 series ClearSpeed accelerator measured in past work is used to establish a baseline. We show comparable performance between a single CSX600 board and the OpenMP solution in order to predict the scaling of the ClearSpeed accelerator, with a similar scheduling overhead to the OpenMP implementation. We developed two implementations of the Smith-Waterman algorithm based on the extended ClearSpeed Implementation. One was developed using stack memory and the other using heap memory. We show that the while the OpenMP solution is faster at small problem sizes using the stack memory, it is limited in the problem size it can handle. We also show that for larger problem sizes to be handled in OpenMP it comes at a cost of a memory initialization overhead using heap memory and the ClearSpeed solution is faster when comparing to the heap memory implementation. We predict the future ClearSpeed solution of a much larger board would excel, quickly overtaking the OpenMP implementation for larger, more realistic problem sizes because of the distributed memory model it uses.
Johnnie Baker (Advisor)
Shannon Steinfadt (Committee Member)
Arvind Bansal (Committee Member)
Arden Ruttan (Committee Member)
36 p.
Computer Science
parallel; smith-waterman; dna; sequencing; dna-sequencing; swamp; cleerspeed; openmp; cn; sequence-alignment; simd;

Recommended Citations

Citations

  • Cuevas, T. L. (2015). A PAIRWISE COMPARISON OF DNA SEQUENCE ALIGNMENT USING AN OPENMP IMPLEMENTATION OF THE SWAMP PARALLEL SMITH-WATERMAN ALGORITHM [Master's thesis, Kent State University]. OhioLINK Electronic Theses and Dissertations Center. http://rave.ohiolink.edu/etdc/view?acc_num=kent1429528937

    APA Style (7th edition)

  • Cuevas, Tristan. A PAIRWISE COMPARISON OF DNA SEQUENCE ALIGNMENT USING AN OPENMP IMPLEMENTATION OF THE SWAMP PARALLEL SMITH-WATERMAN ALGORITHM. 2015. Kent State University, Master's thesis. OhioLINK Electronic Theses and Dissertations Center, http://rave.ohiolink.edu/etdc/view?acc_num=kent1429528937.

    MLA Style (8th edition)

  • Cuevas, Tristan. "A PAIRWISE COMPARISON OF DNA SEQUENCE ALIGNMENT USING AN OPENMP IMPLEMENTATION OF THE SWAMP PARALLEL SMITH-WATERMAN ALGORITHM." Master's thesis, Kent State University, 2015. http://rave.ohiolink.edu/etdc/view?acc_num=kent1429528937

    Chicago Manual of Style (17th edition)

kent1429528937
1,425
© 2015, all rights reserved.
This open access ETD is published by Kent State University and OhioLINK.