PopGeV: a web-based large-scale population genome browser

	PopGeV: a web-based large-scale population genome browser
	X. Y. Shi; J. Peng; X. H. Yu; X. H. Zhang; D. Y. Li; B. H. Liu; F. J. Kong; X. H. Yuan
刊名	Bioinformatics
	2015
卷号	31 期号:18 页码:3048-3050
通讯作者	袁晓辉
中文摘要	Motivation: The development of high-throughput sequencing technology has made it possible for more and more researchers to use population sequencing data to mine genes associated with specific traits. However, the massive amounts of sequencing data have also brought new challenges to the researchers. The question of how to browse population genomic data in an easy and intuitive manner must be addressed. Web-based genome browsers allow user to conveniently view the results of genomic analyses, but heavy usage can reduce the response speed of the webpage, which limits its usefulness in the display of large-scale genome data. IndexedDB technology is a good solution to this problem; it supports web browsers and so creates local databases. In this way, data can be read from the local storage, achieving a smooth display of population genomic data. Results: PopGeV has the following characteristics. First, it uses a new encoding method for compression of population SNP and INDEL data. IndexedDB technology is used to download the results to local storage so that users can browse the results smoothly even when the network traffic is heavy. Second, PopGeV identify similar genomic regions between two individuals based on SNP data. Population diversity indexes are calculated when comparing two populations. Third, user defined annotation information can be integrated for user-friendly mining of gene functions. Simulation shows that PopGeV can smoothly display analysis results of population genome containing over 500 individuals with 2 millions SNP data.
内容类型	期刊论文
源URL	[http://159.226.123.10/handle/131322/6530]
专题	东北地理与农业生态研究所_大豆分子育种学科组_期刊论文
推荐引用方式 GB/T 7714	X. Y. Shi,J. Peng,X. H. Yu,et al. PopGeV: a web-based large-scale population genome browser[J]. Bioinformatics,2015,31(18):3048-3050.
APA	X. Y. Shi.,J. Peng.,X. H. Yu.,X. H. Zhang.,D. Y. Li.,...&X. H. Yuan.(2015).PopGeV: a web-based large-scale population genome browser.Bioinformatics,31(18),3048-3050.
MLA	X. Y. Shi,et al."PopGeV: a web-based large-scale population genome browser".Bioinformatics 31.18(2015):3048-3050.