当前位置: X-MOL 学术Mobile DNA › 论文详情
A benchmark of transposon insertion detection tools using real data
Mobile DNA ( IF 3.161 ) Pub Date : 2019-12-30 , DOI: 10.1186/s13100-019-0197-9
Pol Vendrell-Mir; Fabio Barteri; Miriam Merenciano; Josefa González; Josep M. Casacuberta; Raúl Castanera

Transposable elements (TEs) are an important source of genomic variability in eukaryotic genomes. Their activity impacts genome architecture and gene expression and can lead to drastic phenotypic changes. Therefore, identifying TE polymorphisms is key to better understand the link between genotype and phenotype. However, most genotype-to-phenotype analyses have concentrated on single nucleotide polymorphisms as they are easier to reliable detect using short-read data. Many bioinformatic tools have been developed to identify transposon insertions from resequencing data using short reads. Nevertheless, the performance of most of these tools has been tested using simulated insertions, which do not accurately reproduce the complexity of natural insertions. We have overcome this limitation by building a dataset of insertions from the comparison of two high-quality rice genomes, followed by extensive manual curation. This dataset contains validated insertions of two very different types of TEs, LTR-retrotransposons and MITEs. Using this dataset, we have benchmarked the sensitivity and precision of 12 commonly used tools, and our results suggest that in general their sensitivity was previously overestimated when using simulated data. Our results also show that, increasing coverage leads to a better sensitivity but with a cost in precision. Moreover, we found important differences in tool performance, with some tools performing better on a specific type of TEs. We have also used two sets of experimentally validated insertions in Drosophila and humans and show that this trend is maintained in genomes of different size and complexity. We discuss the possible choice of tools depending on the goals of the study and show that the appropriate combination of tools could be an option for most approaches, increasing the sensitivity while maintaining a good precision.
更新日期:2019-12-30

 

全部期刊列表>>
材料学研究精选
Springer Nature Live 产业与创新线上学术论坛
胸腔和胸部成像专题
自然科研论文编辑服务
ACS ES&T Engineering
ACS ES&T Water
屿渡论文,编辑服务
杨超勇
周一歌
华东师范大学
段炼
清华大学
中科大
唐勇
跟Nature、Science文章学绘图
隐藏1h前已浏览文章
中洪博元
课题组网站
新版X-MOL期刊搜索和高级搜索功能介绍
ACS材料视界
x-mol收录
福州大学
南京大学
王杰
左智伟
电子显微学
何凤
洛杉矶分校
吴杰
赵延川
试剂库存
天合科研
down
wechat
bug