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Exact parallel alignment of megabase genomic sequences with tunable work distribution

机译:megabase基因组序列与可调工作分布的完全平行排列

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摘要

Sequence Alignment is a basic operation in Bioinformatics that is performed thousands of times, on daily basis. The exact methods for pairwise alignment have quadratic time complexity. For this reason, heuristic methods such as BLAST are widely used. To obtain exact results faster, parallel strategies have been proposed but most of them fail to align huge biological sequences. This happens because not only the quadratic time must be considered but also the space should be reduced. In this paper, we evaluate the performance of Z-align, a parallel exact strategy that runs in user-restricted memory space. Also, we propose and evaluate a tunable work distribution mechanism. The results obtained in two clusters show that two sequences of size 24MBP (Mega Base Pairs) and 23MBP, respectively, were successfully aligned with Z-align. Also, in order to align two 3MBP sequences, a speedup of 34.35 was achieved for 64 processors. The evaluation of our work distribution mechanism shows that the execution times can be sensibly reduced when appropriate parameters are chosen. Finally, when comparing Z-align with BLAST, it is clear that, in many cases, Z-align is able to produce alignments with higher score.
机译:序列比对是生物信息学中的一项基本操作,每天执行数千次。成对对齐的确切方法具有二次时间复杂度。因此,诸如BLAST的启发式方法被广泛使用。为了更快地获得准确的结果,已经提出了并行策略,但是大多数策略都无法比对巨大的生物学序列。发生这种情况是因为不仅必须考虑二次时间,而且还应减少空间。在本文中,我们评估了Z-align的性能,Z-align是在用户限制的内存空间中运行的并行精确策略。此外,我们提出并评估了可调工作分配机制。在两个聚类中获得的结果表明,大小分别为24MBP(兆碱基对)和23MBP的两个序列已通过Z-align成功比对。另外,为了对齐两个3MBP序列,对64个处理器实现了34.35的加速。我们对工作分配机制的评估表明,选择适当的参数可以显着减少执行时间。最后,将Z-align与BLAST进行比较时,很明显,在许多情况下,Z-align能够产生具有更高分数的比对。

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