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Open Access Software

CGAP: a new comprehensive platform for the comparative analysis of chloroplast genomes

Jinkui Cheng1, Xu Zeng1, Guomin Ren1 and Zhihua Liu12*

Author Affiliations

1 Department of Computational Biology and Bioinformatics, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100193, China

2 Nanjing Forestry University, Nanjing, 210037, China

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BMC Bioinformatics 2013, 14:95  doi:10.1186/1471-2105-14-95

Published: 14 March 2013

Abstract

Background

Chloroplast is an essential organelle in plants which contains independent genome. Chloroplast genomes have been widely used for plant phylogenetic inference recently. The number of complete chloroplast genomes increases rapidly with the development of various genome sequencing projects. However, no comprehensive platform or tool has been developed for the comparative and phylogenetic analysis of chloroplast genomes. Thus, we constructed a comprehensive platform for the comparative and phylogenetic analysis of complete chloroplast genomes which was named as chloroplast genome analysis platform (CGAP).

Results

CGAP is an interactive web-based platform which was designed for the comparative analysis of complete chloroplast genomes. CGAP integrated genome collection, visualization, content comparison, phylogeny analysis and annotation functions together. CGAP implemented four web servers including creating complete and regional genome maps of high quality, comparing genome features, constructing phylogenetic trees using complete genome sequences, and annotating draft chloroplast genomes submitted by users.

Conclusions

Both CGAP and source code are available at http://www.herbbol.org:8000/chloroplast webcite. CGAP will facilitate the collection, visualization, comparison and annotation of complete chloroplast genomes. Users can customize the comparative and phylogenetic analysis using their own unpublished chloroplast genomes.

Keywords:
Chloroplast genomes; Comparative and phylogenetic analysis; Web-based platform