QQ客服 官方微博 反馈留言

	Itis, a bioinformatics tool for accurate identification of transposon insertion sites using next-generation sequencing data
	Jiang,Chuan1,2; Chen,Chao1,2; Huang,Ziyue1; Liu,Renyi1; Verdier,Jerome1
刊名	Bmc bioinformatics
	2015-03-05
卷号	16期号:1
关键词	Transposable elements Insertion sites Itis Forward genetics Tnt1 Medicago truncatula
ISSN号	1471-2105
DOI	10.1186/s12859-015-0507-2
通讯作者	Liu,renyi(ryliu@sibs.ac.cn) ; Verdier,jerome(javerdier@sibs.ac.cn)
英文摘要	Abstractbackgroundtransposable elements constitute an important part of the genome and are essential in adaptive mechanisms. transposition events associated with phenotypic changes occur naturally or are induced in insertional mutant populations. transposon mutagenesis results in multiple random insertions and recovery of most/all the insertions is critical for forward genetics study. using genome next-generation sequencing data and appropriate bioinformatics tool, it is plausible to accurately identify transposon insertion sites, which could provide candidate causal mutations for desired phenotypes for further functional validation.resultswe developed a novel bioinformatics tool, itis (identification of transposon insertion sites), for localizing transposon insertion sites within a genome. it takes next-generation genome re-sequencing data (ngs data), transposon sequence, and reference genome sequence as input, and generates a list of highly reliable candidate insertion sites as well as zygosity information of each insertion. using a simulated dataset and a case study based on an insertional mutant line from medicago truncatula, we showed that itis performed better in terms of sensitivity and specificity than other similar algorithms such as relocate, retroseq, temp and tif. with the case study data, we demonstrated the efficiency of itis by validating the presence and zygosity of predicted insertion sites of the tnt1 transposon within a complex plant system, m. truncatula.conclusionthis study showed that itis is a robust and powerful tool for forward genetic studies in identifying transposable element insertions causing phenotypes. itis is suitable in various systems such as cell culture, bacteria, yeast, insect, mammal and plant.
语种	英语
出版者	BioMed Central
WOS记录号	BMC:10.1186/S12859-015-0507-2
内容类型	期刊论文
URI标识	http://www.corc.org.cn/handle/1471x/2374289
专题	中国科学院大学
通讯作者	Liu,Renyi; Verdier,Jerome
作者单位	1.Shanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences 2.University of Chinese Academy of Sciences
推荐引用方式 GB/T 7714	Jiang,Chuan,Chen,Chao,Huang,Ziyue,et al. Itis, a bioinformatics tool for accurate identification of transposon insertion sites using next-generation sequencing data[J]. Bmc bioinformatics,2015,16(1).
APA	Jiang,Chuan,Chen,Chao,Huang,Ziyue,Liu,Renyi,&Verdier,Jerome.(2015).Itis, a bioinformatics tool for accurate identification of transposon insertion sites using next-generation sequencing data.Bmc bioinformatics,16(1).
MLA	Jiang,Chuan,et al."Itis, a bioinformatics tool for accurate identification of transposon insertion sites using next-generation sequencing data".Bmc bioinformatics 16.1(2015).

个性服务

查看访问统计

相关权益政策

暂无数据

收藏/分享

除非特别说明，本系统中所有内容都受版权保护，并保留所有权利。