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Allows the semi-automatic and complete annotation of a chloroplast genome sequence, and the visualization, editing and analysis of the annotation results. 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. CpGAVAS will become an indispensable tool for researchers studying chloroplast genomes.

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CpGAVAS classification

  • Plants

CpGAVAS specifications

Web user interface
Input data:
Complete chloroplast genome sequence
Output format:
Restrictions to use:
Output data:
The annotation results in GFF3 format can be edited using any compatible annotation editing tools.
Computer skills:

CpGAVAS support


  • Chang Liu <>


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Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China

Funding source(s)

This work was supported by a start fund from the Chinese Academy of Medical Science (No. 431118) granted to C. Liu, Basic Scientific Research Operation Grants for State-Level Public Welfare Scientific Research Initiatives (No. YZ-12-04 granted to C. Liu), Research grant for returned Overseas Chinese Scholars, Ministry of Human Resources (No. 431207) granted to C. Liu, a grant from National Science Foundation (No. 81202859) to HM. Chen and Program for Changjiang Scholars and Innovative Research Team in University of Ministry of Education of China (No. IRT1150).

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