CPGAVAS2, an integrated plastome sequence annotator and analyzer
CPGAVAS2, an integrated plastome sequence annotator and analyzer
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DOI：
10.1093/nar/gkz345
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发表时间：
2019-07-02
影响因子：
14.9
通讯作者：
Liu, Chang
中科院分区：
文献类型：
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作者：
Shi, Linchun;Chen, Haimei;Liu, Chang
我们之前开发了一个网络服务器CPGAVAS，用于质体组序列的注释、可视化和GenBank提交。在这里，我们将服务器升级到CPGAVAS2，以解决以下挑战：(I)参考序列中不准确的注释可能导致错误的传播；(Ii)基因petB、petd和rps16的小外显子以及反式剪接基因rps12的注释困难；(Iii)缺乏对其他基因组特征及其可视化的注释，如重复元件；以及(Iv)缺乏用于质体体多样性分析的模块。特别是，CPGAVAS2提供了两个用于质体组注释的参考数据集。第一个数据集包含43个质体体，其注释已被RNA-seq数据验证或更正。第二个包含2544个经过序列比对的质粒体。还实现了两个新的算法来正确注释小外显子和反式剪接基因。识别串联和分散的重复序列，其结果与注释的基因一起显示在圆形地图上。可以上传DNA-seq和RNA-seq数据，以识别单核苷酸多态位点和RNA编辑位点。两个案例研究的结果表明，CPGAVAS2比其他几个服务器具有更好的标注效果。CPGAVAS2很可能成为质体组研究不可或缺的工具，可从http://www.herbalgenomics.org/cpgavas2.获取
We previously developed a web server CPGAVAS for annotation, visualization and GenBank submission of plastome sequences. Here, we upgrade the server into CPGAVAS2 to address the following challenges: (i) inaccurate annotation in the reference sequence likely causing the propagation of errors; (ii) difficulty in the annotation of small exons of genes petB, petD and rps16 and trans-splicing gene rps12; (iii) lack of annotation for other genome features and their visualization, such as repeat elements; and (iv) lack of modules for diversity analysis of plastomes. In particular, CPGAVAS2 provides two reference datasets for plastome annotation. The first dataset contains 43 plastomes whose annotation have been validated or corrected by RNA-seq data. The second one contains 2544 plastomes curated with sequence alignment. Two new algorithms are also implemented to correctly annotate small exons and trans-splicing genes. Tandem and dispersed repeats are identified, whose results are displayed on a circular map together with the annotated genes. DNA-seq and RNA-seq data can be uploaded for identification of single-nucleotide polymorphism sites and RNA-editing sites. The results of two case studies show that CPGAVAS2 annotates better than several other servers. CPGAVAS2 will likely become an indispensible tool for plastome research and can be accessed from http://www.herbalgenomics.org/cpgavas2.