Short read DNA fragment anchoring algorithm

doi:10.1186/1471-2105-10-S1-S17

	Short read DNA fragment anchoring algorithm
	Wang, Wendi; Zhang, Peiheng; Liu, Xinchun
	2009-01-30
发表期刊	BMC BIOINFORMATICS
ISSN	1471-2105
卷号	10 页码:11
摘要	Background: The emerging next-generation sequencing method based on PCR technology boosts genome sequencing speed considerably, the expense is also get decreased. It has been utilized to address a broad range of bioinformatics problems. Limited by reliable output sequence length of next-generation sequencing technologies, we are confined to study gene fragments with 30 similar to 50 bps in general and it is relatively shorter than traditional gene fragment length. Anchoring gene fragments in long reference sequence is an essential and prerequisite step for further assembly and analysis works. Due to the sheer number of fragments produced by next-generation sequencing technologies and the huge size of reference sequences, anchoring would rapidly becoming a computational bottleneck. Results and discussion: We compared algorithm efficiency on BLAT, SOAP and EMBF. The efficiency is defined as the count of total output results divided by time consumed to retrieve them. The data show that our algorithm EMBF have 3 similar to 4 times efficiency advantage over SOAP, and at least 150 times over BLAT. Moreover, when the reference sequence size is increased, the efficiency of SOAP will get degraded as far as 30%, while EMBF have preferable increasing tendency. Conclusion: In conclusion, we deem that EMBF is more suitable for short fragment anchoring problem where result completeness and accuracy is predominant and the reference sequences are relatively large.
DOI	10.1186/1471-2105-10-S1-S17
收录类别	SCI
语种	英语
WOS研究方向	Biochemistry & Molecular Biology ; Biotechnology & Applied Microbiology ; Mathematical & Computational Biology
WOS类目	Biochemical Research Methods ; Biotechnology & Applied Microbiology ; Mathematical & Computational Biology
WOS记录号	WOS:000265601900017
出版者	BIOMED CENTRAL LTD
引用统计	被引频次：7[WOS] [WOS记录] [WOS相关记录]
文献类型	期刊论文
条目标识符	http://119.78.100.204/handle/2XEOYT63/11820
专题	中国科学院计算技术研究所期刊论文_英文
通讯作者	Wang, Wendi
作者单位	Chinese Acad Sci, Inst Comp Technol, Beijing 100190, Peoples R China
推荐引用方式 GB/T 7714	Wang, Wendi,Zhang, Peiheng,Liu, Xinchun. Short read DNA fragment anchoring algorithm[J]. BMC BIOINFORMATICS,2009,10:11.
APA	Wang, Wendi,Zhang, Peiheng,&Liu, Xinchun.(2009).Short read DNA fragment anchoring algorithm.BMC BIOINFORMATICS,10,11.
MLA	Wang, Wendi,et al."Short read DNA fragment anchoring algorithm".BMC BIOINFORMATICS 10(2009):11.