Development and implementation of CARAS algorithm for automatic annotation, visualization, and GenBank submission of chloroplast genome sequences

We present CARAS, a web server that allows the automatic annotation of a chloroplast genome sequence, and the visualization and editing of the annotation results interactively and in real-time. CARAS accepts a complete chloroplast genome sequence as input. First, it accurately predicts protein-coding sequences and exon-intron structures by combining the results from two types of annotation approaches: ab initio prediction algorithms and similarity based methods. Second, tRNA genes and inverted repeats are identified using tRNAscan and vmatch. Using 220 chloroplast genome sequences as test, we show that CARAS outperforms a similar application DOGMA overall. Third, the annotation results are presented as a circular map that includes the name, location, orientation, and length of the various features. A Flex-based module is implemented, allowing the users to add, delete, and edit the features on-line. The results are stored on the server and can be retrieved from a given URL. Users also have options to download the annotation results in GFF3 format for further analyses in other third party software tools or in JPEG format for publication. Finally, CARAS can be used to create a Sequin file for GenBank submission of the annotated genome sequence. CARAS is freely available at http://caras.bicoup.com, and it will significantly facilitate research work involving chloroplast genomes.