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| PRAM和LARPBS模型上有向序列翻转距离并行算法 |
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沈一飞1,2, 陈国良1,2, 张强锋1,2
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1.中国科学技术大学,计算机科学技术系,安徽,合肥,230027;2.国家高性能计算中心(合肥),安徽,合肥,230027
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| 摘要: |
| 分别在两种重要并行计算模型中给出计算有向基因组排列的反转距离新的并行算法.基于Hannenhalli和Pevzner理论,分3个主要部分设计并行算法:构建断点图、计算断点图中圈数、计算断点图中障碍的数目.在CREW-PRAM模型上,算法使用O(n2)处理器,时间复杂度为O(log2n);在基于流水光总线的可重构线性阵列系统(linear array with a reconfigurable pipelined bus system, LARPBS)模型上,算法使用O(n3)处理器,计算时间复杂度为O(logn). |
| 关键词: 并行算法 光总线并行模型 反转距离 基因组重排 序列比较 CREW-PRAM模型 |
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| 基金项目:Supported by the Key Project of the National Natural Science Foundation of China under Grant No.60533020 (国家自然科学基金重点项目) |
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| Parallel Algorithms for Reversal Distance of Permutations on PRAM and LARPBS |
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SHEN Yi-Fei,CHEN Guo-Liang,ZHANG Qiang-Feng
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| Abstract: |
| This paper presents two parallel algorithms to compute reversal distance of two signed permutations on different models. These two algorithms are based on Hannenhalli and Pevzner's theory and composed of three key steps: Construct break point graph, compute the number of cycles in break point graph and compute the number of hurdles in break point graph. The first algorithm runs in O(log2n) time using O(n2) processors in SIMD-CREW model. The second one can solve the problem in O(logn) bus cycles by using O(n3) processors on the linear array with a reconfigurable pipelined bus system (LARPBS). |
| Key words: parallel algorithm optical bus parallel model reversal distance genome rearrangements sequence comparison CREW-PRAM model |
