| 多序列比对软件T-Coffee的并行化设计与实现 |
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| 引用本文： | 靳新,骆志刚,蒋晓舟,王金华,张雯.多序列比对软件T-Coffee的并行化设计与实现[J].计算机应用与软件,2008,25(4):221-223. |
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| 作者姓名： | 靳新 骆志刚 蒋晓舟 王金华 张雯 |
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| 作者单位： | 国防科学技术大学并行与分布处理国家重点实验室,湖南,长沙,410073 |
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| 摘 要： | T-Coffee是广泛用于核酸或氨基酸的多序列比对工具.它通过生成基本信息库,扩展库,生成指导树,渐近式比对四个阶段来完成多序列的比对.分析了T-Coffee串行算法及其复杂度,并提出了基于SMP机的并行化版本.目标是使其充分并行化,实验结果表明它明显的提高了性能,并得到了很好的相对加速比.
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| 关 键 词： | 全局比对 局部比对 渐近式算法 共享内存多处理机 |
| 修稿时间： | 2006年8月11日 |
DESIGN AND IMPLEMENTATION OF PARALLELISM OF MULTIPLE SEQUENCE ALIGNMENT SOFTWARE T-COFFEE |
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| Jin Xin,Luo Zhigang,Jiang Xiaozhou,Wang Jinhua,Zhang Wen.DESIGN AND IMPLEMENTATION OF PARALLELISM OF MULTIPLE SEQUENCE ALIGNMENT SOFTWARE T-COFFEE[J].Computer Applications and Software,2008,25(4):221-223. |
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| Authors: | Jin Xin Luo Zhigang Jiang Xiaozhou Wang Jinhua Zhang Wen |
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| Affiliation: | Jin Xin Luo Zhigang Jiang Xiaozhou Wang Jinhua Zhang Wen(National Laboratory of Parallel , Distributed Processing,NUDT,Changsha 410073,Hunan,China) |
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| Abstract: | T-Coffee is the most widely used tool for aligning multiple protein or nucleotide sequences.The alignment is achieved via four stages:primary library generation,extended library generation,guide tree generation and progressive alignment.The complexity of T-Coffee sequence algorithm is analyzed,and a parallel version for T-Coffee based on SMP is presented with an aim to realized full parallelism.The experimental results show that the parallel version improves the performance significantly,and a considerable ... |
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| Keywords: | Global alignment Local alignment Progressive algorithm SMP |
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