Abstract
BackgroundChloroplast 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).ResultsCGAP 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.ConclusionsBoth CGAP and source code are available at http://www.herbbol.org:8000/chloroplast. 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 Users can customize the comparative and phylogenetic analysis using their own unpublished chloroplast genomes.
Highlights
Chloroplast is an essential organelle in plants which contains independent genome
As the number of sequenced chloroplast genomes increases rapidly, bioinformatics tools become more critical for the analysis of complete chloroplast genomes
According to the annotation information stored in the GenBank format file, chloroplast genome analysis platform (CGAP) extracted all types of genome features including Gene, CDS, tRNA, rRNA, Exon, Intron, Promoter, RepeatRegion, StemLoop, -10 Signal and -35 Signal
Summary
Chloroplast is an essential organelle in plants which contains independent genome. No comprehensive platform or tool has been developed for the comparative and phylogenetic analysis of chloroplast genomes. Because of the conserved nature, As the number of sequenced chloroplast genomes increases rapidly, bioinformatics tools become more critical for the analysis of complete chloroplast genomes. Edu/) is a web-based annotation tool for chloroplast and mitochondrial genomes [10]. There is no comprehensive platform or tool which can be used for the comparative and phylogenetic analysis of chloroplast genomes. We aim to construct a platform which integrates genome collection, visualization, comparison, phylogenetic analysis and annotation functions together. It will facilitate the comparative and phylogenetic analysis of complete chloroplast genomes
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