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CpGAVAS, an integrated web server for the annotation, visualization, analysis, and GenBank submission of completely sequenced chloroplast genome sequences

Chang Liu1*, Linchun Shi1, Yingjie Zhu1, Haimei Chen1, Jianhui Zhang1, Xiaohan Lin1 and Xiaojun Guan2

Author Affiliations

1 Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, 151 MaLianWa North Road, Haidian District, Beijing 100191, People’s Republic of China

2 Center for Bioinformatics, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA

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BMC Genomics 2012, 13:715  doi:10.1186/1471-2164-13-715

Published: 20 December 2012



The 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.


We 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.


CPGAVAS 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 webcite.

Chloroplast genome; Annotation; Web server; CPGAVAS