CpGAVAS, an integrated web server for the annotation, visualization, analysis, and GenBank submission of completely sequenced chloroplast genome sequences.
CpGAVAS, an integrated web server for the annotation, visualization, analysis, and GenBank submission of completely sequenced chloroplast genome sequences.
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CpGAVAS，一个集成的网络服务器，用于注释、可视化、分析和 GenBank 提交完整测序的叶绿体基因组序列
DOI：
10.1186/1471-2164-13-715
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发表时间：
2012-12-20
期刊：
影响因子：
4.4
通讯作者：
Guan X
中科院分区：
文献类型：
--
作者：
Liu C;Shi L;Zhu Y;Chen H;Zhang J;Lin X;Guan X
背景叶绿体基因组的全序列为物种的进化提供了丰富的信息。随着下一代测序技术的发展，叶绿体基因组全序列的数量将呈指数级增长，迫切需要强大的计算工具对基因组序列进行注释。服务器接受完整的叶绿体基因组序列作为输入。首先，它预测蛋白质编码和rRNA基因的基础上，最相似的，全长蛋白质，cDNA和rRNA序列的识别和映射，通过整合结果从Blastx，Blastin，protein2genome和est2genome程序。其次，分别用tRNAscan、ARAGORN和vmatch鉴定tRNA基因和反向重复序列（IR）。第三，计算注释基因组的汇总统计量。第四，它生成一个可供发布的环形地图。第五，它可以创建一个Sequin文件提交GenBank。最后，它允许提取给定基因和物种列表的蛋白质和mRNA序列。GFF3格式的注释结果可以使用任何兼容的注释编辑工具进行编辑。编辑后的注释可以上传到CPGAVAS，以便重复更新和重新分析。使用已知的叶绿体基因组序列作为测试集，我们表明，CPGAVAS执行重复到另一个应用程序DOGMA，同时具有几个上级functionals.ConclusionsCPGAVAS允许半自动和完整的叶绿体基因组序列的注释，以及注释结果的可视化，编辑和分析。它将成为研究叶绿体基因组的研究人员不可或缺的工具。该软件可从以下网址免费获取： http://www.herbalgenomics.org/cpgavas .
BackgroundThe complete sequences of chloroplast genomes provide wealthy information regarding the evolutionary history of species. With the advance of next-generation sequencing technology, the number of completely sequenced chloroplast genomes is expected to increase exponentially, powerful computational tools annotating the genome sequences are in urgent need.ResultsWe have developed a web server CPGAVAS. The server accepts a complete chloroplast genome sequence as input. First, it predicts protein-coding and rRNA genes based on the identification and mapping of the most similar, full-length protein, cDNA and rRNA sequences by integrating results from Blastx, Blastn, protein2genome and est2genome programs. Second, tRNA genes and inverted repeats (IR) are identified using tRNAscan, ARAGORN and vmatch respectively. Third, it calculates the summary statistics for the annotated genome. Fourth, it generates a circular map ready for publication. Fifth, it can create a Sequin file for GenBank submission. Last, it allows the extractions of protein and mRNA sequences for given list of genes and species. The annotation results in GFF3 format can be edited using any compatible annotation editing tools. The edited annotations can then be uploaded to CPGAVAS for update and re-analyses repeatedly. Using known chloroplast genome sequences as test set, we show that CPGAVAS performs comparably to another application DOGMA, while having several superior functionalities.ConclusionsCPGAVAS allows the semi-automatic and complete annotation of a chloroplast genome sequence, and the visualization, editing and analysis of the annotation results. It will become an indispensible tool for researchers studying chloroplast genomes. The software is freely accessible from http://www.herbalgenomics.org/cpgavas .
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影响因子：
14.9
作者：
Timmermans MJ;Dodsworth S;Culverwell CL;Bocak L;Ahrens D;Littlewood DT;Pons J;Vogler AP
通讯作者：
Vogler AP
影响因子：
2.5
作者：
Lohse, Marc;Drechsel, Oliver;Bock, Ralph
通讯作者：
Bock, Ralph
影响因子：
5.8
作者：
Wyman, SK;Jansen, RK;Boore, JL
通讯作者：
Boore, JL
影响因子：
3.8
作者：
Kim, Young-Kyu;Park, Chong-wook;Kim, Ki-Joong
通讯作者：
Kim, Ki-Joong
影响因子：
7
作者：
Skinner, Mitchell E.;Uzilov, Andrew V.;Holmes, Ian H.
通讯作者：
Holmes, Ian H.