Load Balancing and Parallel Multiple Sequence Alignment with Tree Accumulation
نویسندگان
چکیده
Multiple sequence alignment program, ClustalW, is time consuming, however, commonly used to compare the protein sequences. ClustalW includes two main time consuming parts: pairwise alignment and progressive alignment. Due to the irregular computation based on tree in progressive alignment, available parallel programs can not achieve reasonable speedups for large scale number of sequences. In this paper, progressive alignment is reduced to tree accumulation problem. Load balancing is ignored in previous efficient parallel tree accumulations. We proposed a load balancing strategy for parallelizing tree accumulation in progressive alignment. The new parallel progressive alignment algorithm reducing to tree accumulation with load balancing reduced the overall running time greatly and achieved reasonable speedups.
منابع مشابه
Parallel Sequence Analysis under Three Load Balancing Strategies
Retrieving homologous sequences from existing databases is very important for the biomedical research community. In this project, we implemented four sequence alignment algorithms (general gap penalty, affine gap penalty, general gap penalty with mid-point and affine gap penalty with midpoint) to look for nearly optimum aligned sequences in the database for nucleic acid sequences (i.e. DNA/RNA ...
متن کاملParallel R-Tree Spatial Join for a Shared-Nothing Architecture
The growing importance of spatial data has made it imperative that spatial operations be executed efficiently. The most expensive operation is the join for spatial databases. This paper proposes a Replicated Parallel Packed R-tree and its use in performing the parallel R-tree join. We examine performance using the Digital Chart of the World Data on a shared nothing machine. Our experimental res...
متن کاملPARUS: A Parallel Programming Framework for Heterogeneous Multiprocessor Systems
PARUS is a parallel programing framework that allows building parallel programs in data flow graph notation. The data flow graph is created by developer either manually or automatically with the help of a script. The graph is then converted to C++/MPI source code and linked with the PARUS runtime system. The next step is the parallel program execution on a cluster or multiprocessor system. PARU...
متن کاملA Hybrid Unconscious Search Algorithm for Mixed-model Assembly Line Balancing Problem with SDST, Parallel Workstation and Learning Effect
Due to the variety of products, simultaneous production of different models has an important role in production systems. Moreover, considering the realistic constraints in designing production lines attracted a lot of attentions in recent researches. Since the assembly line balancing problem is NP-hard, efficient methods are needed to solve this kind of problems. In this study, a new hybrid met...
متن کاملA balanced accumulation scheme for parallel PDE solvers
We present a load balancing technique for a boundary data accumulation algorithm for non-overlapping domain decompositions. The technique is used to speed up a parallel conjugate gradient algorithm with an algebraic multigrid preconditioner to solve a potential problem on an unstructured tetrahedral finite element mesh. The optimized accumulation algorithm significantly improves the performance...
متن کامل