SWAMP+ [electronic resource] : multiple subsequence alignment using associative massive parallelism
- Published
- Washington, D.C. : United States. Dept. of Energy, 2010.
Oak Ridge, Tenn. : Distributed by the Office of Scientific and Technical Information, U.S. Dept. of Energy. - Additional Creators
- Los Alamos National Laboratory, United States. Department of Energy, and United States. Department of Energy. Office of Scientific and Technical Information
Access Online
- Restrictions on Access
- Free-to-read Unrestricted online access
- Summary
- A new parallel algorithm SWAMP+ incorporates the Smith-Waterman sequence alignment on an associative parallel model known as ASC. It is a highly sensitive parallel approach that expands traditional pairwise sequence alignment. This is the first parallel algorithm to provide multiple non-overlapping, non-intersecting subsequence alignments with the accuracy of Smith-Waterman. The efficient algorithm provides multiple alignments similar to BLAST while creating a better workflow for the end users. The parallel portions of the code run in O(m+n) time using m processors. When m = n, the algorithmic analysis becomes O(n) with a coefficient of two, yielding a linear speedup. Implementation of the algorithm on the SIMD ClearSpeed CSX620 confirms this theoretical linear speedup with real timings.
- Report Numbers
- E 1.99:la-ur-10-07036
E 1.99: la-ur-10-7036
la-ur-10-7036
la-ur-10-07036 - Subject(s)
- Other Subject(s)
- Note
- Published through SciTech Connect.
10/18/2010.
"la-ur-10-07036"
" la-ur-10-7036"
IEEE international parallel & Distributed processing symposium ; May 16, 2011 ; Anchorage, Ak.
Steinfadt, Shannon Irene; Baker, Johnnie W. - Funding Information
- AC52-06NA25396
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