کد مقاله کد نشریه سال انتشار مقاله انگلیسی نسخه تمام متن
432102 688708 2009 12 صفحه PDF دانلود رایگان
عنوان انگلیسی مقاله ISI
A domain decomposition strategy for alignment of multiple biological sequences on multiprocessor platforms
موضوعات مرتبط
مهندسی و علوم پایه مهندسی کامپیوتر نظریه محاسباتی و ریاضیات
پیش نمایش صفحه اول مقاله
A domain decomposition strategy for alignment of multiple biological sequences on multiprocessor platforms
چکیده انگلیسی

Multiple Sequences Alignment (MSA) of biological sequences is a fundamental problem in computational biology due to its critical significance in wide ranging applications including haplotype reconstruction, sequence homology, phylogenetic analysis, and prediction of evolutionary origins. The MSA problem is considered NP-hard and known heuristics for the problem do not scale well with increasing numbers of sequences. On the other hand, with the advent of a new breed of fast sequencing techniques it is now possible to generate thousands of sequences very quickly. For rapid sequence analysis, it is therefore desirable to develop fast MSA algorithms that scale well with an increase in the dataset size. In this paper, we present a novel domain decomposition based technique to solve the MSA problem on multiprocessing platforms. The domain decomposition based technique, in addition to yielding better quality, gives enormous advantages in terms of execution time and memory requirements. The proposed strategy allows one to decrease the time complexity of any known heuristic of O(N)xO(N)x complexity by a factor of O(1/p)xO(1/p)x, where NN is the number of sequences, xx depends on the underlying heuristic approach, and pp is the number of processing nodes. In particular, we propose a highly scalable algorithm, Sample-Align-D, for aligning biological sequences using Muscle system as the underlying heuristic. The proposed algorithm has been implemented on a cluster of workstations using the MPI library. Experimental results for different problem sizes are analyzed in terms of quality of alignment, execution time and speed-up.

ناشر
Database: Elsevier - ScienceDirect (ساینس دایرکت)
Journal: Journal of Parallel and Distributed Computing - Volume 69, Issue 7, July 2009, Pages 666–677
نویسندگان
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