Name
Abstract | ||
|---|---|---|
Multiple sequence alignment is a fundamental and very computationally intensive task in molecular biology. MUSCLE, a new algorithm for creating multiple alignments of protein sequences, achieves a highest rank in accuracy and the fastest speed compared to ClustalW as well as T-Coffee, some widely used tools in multiple sequence alignment. To further accelerate the computations, we present the parallel implementation of MUSCLE in this paper. It is decomposed into several independent modules, which are parallelized with different OpenMP paradigms. We also conduct detailed performance characterization on symmetric multiple processor systems. The experiments show that MUSCLE scales well with the increase of processors, and achieves up to 15.x speedup on 16-way shared memory multiple processor system. |
Year | DOI | Venue |
|---|---|---|
2006 | 10.1109/IPDPS.2006.1639616 | IPDPS |
Keywords | Field | DocType |
multiple processor system,multiple alignment,parallel implementation,muscle scale,detailed performance characterization,computationally intensive task,multiple sequence alignment,different openmp paradigm,protein sequence,16-way shared memory,symmetric multiple processor system,computational biology,concurrent computing,computer science,molecular biophysics,phylogeny,proteins,molecular biology,muscle,shared memory,sequences,parallel processing,acceleration | Shared memory,Computer science,Parallel computing,Parallel processing,Molecular biophysics,Acceleration,Concurrent computing,Multiple sequence alignment,Computation,Speedup,Distributed computing | Conference |
ISBN | Citations | PageRank |
1-4244-0054-6 | 7 | 0.51 |
References | Authors | |
1 | 4 | |
Name | Order | Citations | PageRank |
|---|---|---|---|
| Xi Deng | 1 | 33 | 4.48 |
| Eric Li | 2 | 7 | 0.51 |
| Jiulong Shan | 3 | 25 | 4.15 |
| Wenguang Chen | 4 | 1014 | 70.57 |