Argentin Joris, Bolser Dan, Kersey Paul J, Flicek Paul
Institut de Biologie en Santé, Centre Hospitalier Universitaire (CHU) d'Angers, Angers, France.
European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, United Kingdom.
Front Plant Sci. 2023 Jul 14;14:1103035. doi: 10.3389/fpls.2023.1103035. eCollection 2023.
The DNA Features pipeline is the analysis pipeline at EMBL-EBI that annotates repeat elements, including transposable elements. With Ensembl's goal to stay at the cutting edge of genome annotation, we proved that this pipeline needed an update. We then created a new analysis that allowed the Ensembl database to store the repeat classification from the PGSB repeat classification (Recat). This new dataset was then fetched using Perl scripts and used to prove that the pipeline modification induced a gain in sensitivity. Finally, we performed a comparative analysis of transposable element distribution in all plant species available, raising new questions about transposable elements in certain branches of the taxonomic tree.
DNA特征管道是欧洲生物信息学研究所（EMBL-EBI）用于注释重复元件（包括转座元件）的分析管道。鉴于Ensembl致力于保持基因组注释的前沿地位，我们证明了该管道需要更新。然后，我们创建了一项新分析，使Ensembl数据库能够存储来自PGSB重复分类（Recat）的重复分类。接着，使用Perl脚本获取这个新数据集，并用于证明管道修改提高了敏感性。最后，我们对所有可用植物物种中的转座元件分布进行了比较分析，这引发了关于分类树某些分支中转座元件的新问题。
