Parallelization of Multiple Genome Alignment

机译：多基因组比对的并行化

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摘要

In this work, we implement a genome alignment system which applies parallelization schemes to the ClustalW algorithm and the interface of database querying. Parallel construction of the distance matrices and parallelization of progressive alignment in the ClustalW algorithm are performed on PC-based Linux cluster with message-passing interface libraries. Achieved experiments show good speedup and significant parallel performance.

机译：在这项工作中，我们实现了一个基因组比对系统，该系统将并行化方案应用于ClustalW算法和数据库查询接口。 ClustalW算法中距离矩阵的并行构造和渐进对齐的并行化是在具有消息传递接口库的基于PC的Linux集群上执行的。取得的实验显示出良好的加速比和显着的并行性能。

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来源
《International Conference on High Performance Computing and Communications(HPCC 2005); 20050921-23; Sorrento(IT)》|2005年|P.910-915|共6页
会议地点 Sorrento(IT)
作者
Yiming Li; Cheng-Kai Chen;
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Department of Communication Engineering, National Chiao Tung University, Hsinchu City, Hsinchu 300, Taiwan;

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正文语种 eng
中图分类设计与性能分析;
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专利

1. Multiple Sequence Alignment Based on a Suffix Tree and Center-Star Strategy: A Linear Method for Multiple Nucleotide Sequence Alignment on Spark Parallel Framework [J] . Su Wenhe, Liao Xiangke, Lu Yutong, Journal of computational biology: A journal of computational molecular cell biology . 2017,第12期

机译：基于后缀树和中心星策略的多个序列对齐：一种用于火花并联框架上多个核苷酸序列对准的线性方法
2. Parallelization of MAFFT for large-scale multiple sequence alignments [J] . Nakamura Tsukasa, Yamada Kazunori D., Tomii Kentaro, Bioinformatics . 2018,第14期

机译：MAFFT为大规模多序列对齐的平行化
3. PARALLELIZED HIERARCHICAL EXPECTED MATCHING PROBABILITY FOR MULTIPLE SEQUENCE ALIGNMENT [J] . KEDHAR M, DR. M. RAJASEKHARA BABU, MAYANK G, Journal of Theoretical and Applied Information Technology . 2014,第2期

机译：多序列对齐的并行分层预期匹配概率
4. Parallelization of Multiple Genome Alignment [C] . Yiming Li, Cheng-Kai Chen International Conference on High Performance Computing and Communications . 2005

机译：多个基因组对齐的并行化
5. Computational Methods for Detecting Protein-binding Footprints and Assessing Multiple Genome Sequence Alignments [D] . Chen, Xiaoyu 2011

机译：检测蛋白质结合脚印和评估多个基因组序列比对的计算方法
6. Parallelized pairwise sequence alignment using CUDA on multiple GPUs [O] . Sungbo Jung 2009

机译：在多个GPU上使用CUDA进行并行的成对序列比对
7. Supplemental Information 2: Three multiple alignments are of multiple SARS-CoV-2, SARS-CoV and HKU1 genomes. Three more are multiple alignments of reference human coronaviruses and their relative coronaviruses from bats. [O] . -1

机译：补充信息2：三个多次对准是多个SARS-COV-2，SARS-COV和HKU1基因组。三种参考人冠状病毒和蝙蝠的相对冠状病毒的多次对准。

Parallelization of Multiple Genome Alignment

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