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

BMC Bioinformatics

Jinkui Cheng²  Xu Zeng²  Guomin Ren²  Zhihua Liu¹ 

[1] Nanjing Forestry University, Nanjing, 210037, China

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

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

Others  :  1087940
DOI  :  10.1186/1471-2105-14-95

 received in 2012-10-22, accepted in 2013-02-11,  发布年份 2013

【 摘 要 】

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 Users can customize the comparative and phylogenetic analysis using their own unpublished chloroplast genomes.

【 授权许可】

   
2013 Cheng et al.; licensee BioMed Central Ltd.

【 图 表 】

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