| 基于新测序技术的比对与组装算法 |
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| 引用本文： | 牛北方,张西广,刘涛,郎显宇,陆忠华,迟学斌. 基于新测序技术的比对与组装算法[J]. 计算机工程, 2009, 35(20): 4-6 |
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| 作者姓名： | 牛北方 张西广 刘涛 郎显宇 陆忠华 迟学斌 |
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| 作者单位： | 中国科学院计算机网络信息中心超级计算中心,北京,100190;中国科学院研究生院,北京,100039;中国科学院研究生院,北京,100039;中原工学院计算机学院,郑州,450007;中国科学院北京基因组研究所,北京,100029;中国科学院计算机网络信息中心超级计算中心,北京,100190 |
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| 基金项目： | 国家自然科学基金资助项目"当代并行机的并行算法应用基础研究"，国家自然科学基金资助项目"特征信息发现的并行算法及实现研究"，国家科技部基金资助项目"天文、生物信息和计算化学网格计算应用系统建设" |
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| 摘 要： | 针对新型超高通量测序仪Solexa测序仪所产生的测序片段read的比对与组装问题,提出一种短序列比对与组装算法SRMA,采用对参考序列进行hash的方法,将测序片段read分3段快速、准确地定位于参考序列,对不能定位的read采取从头（Denovo）组装的方法进行组装。测试结果表明SRMA算法具有较高的性能和敏感度,以及良好的应用前景。
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| 关 键 词： | 序列比对 组装 新测序技术 |
| 修稿时间： | |
Alignment and Assembly Algorithm Based on New Sequencing Technique |
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| NIU Bei-fang,ZHANG Xi-guang,LIU Tao,LANG Xian-yu,LU Zhong-hua,CHI Xue-bin. Alignment and Assembly Algorithm Based on New Sequencing Technique[J]. Computer Engineering, 2009, 35(20): 4-6 |
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| Authors: | NIU Bei-fang ZHANG Xi-guang LIU Tao LANG Xian-yu LU Zhong-hua CHI Xue-bin |
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| Affiliation: | (1. Supercomputing Center, Computer Network Information Center, Chinese Academy of Sciences, Beijing 100190; 2. Graduate University of Chinese Academy of Sciences, Beijing 100039; 3. Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 100029; 4. School of Computer Science, Zhongyuan University of Technology, Zhengzhou 450007) |
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| Abstract: | Aiming at the alignment and assembly problem of reads from the new ultra high-throughput sequencer——Solexa sequencing instrument, a new algorithm Short Read Mapping Algorithm(SRMA) for short sequence alignment and assembly is proposed, which uses hash algorithm for reference sequence and exactly locates reads on reference sequences as three segments with high speed. Method of De novo assembly is carried ou to reads which can not be aligned. Test results show that SRMA algorithm has higher performance and sensitivity, and good application future. |
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| Keywords: | sequence alignment assembly new sequencing technique |
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