title: CpGAVAS, an integrated web server for the annotation, visualization, analysis, and GenBank submission of completely sequenced chloroplast genome sequences.
abstract: BACKGROUND
  The complete sequences of chloroplast genomes provide wealthy information regarding the evolutionary history of species. With the advance of next-generation sequencing technology, the number of completely sequenced chloroplast genomes is expected to increase exponentially, powerful computational tools annotating the genome sequences are in urgent need.
  
  
  RESULTS
  We have developed a web server CPGAVAS. The server accepts a complete chloroplast genome sequence as input. 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. The annotation results in GFF3 format can be edited using any compatible annotation editing tools. The edited annotations can then be uploaded to CPGAVAS for update and re-analyses repeatedly. Using known chloroplast genome sequences as test set, we show that CPGAVAS performs comparably to another application DOGMA, while having several superior functionalities.
  
  
  CONCLUSIONS
  CPGAVAS allows the semi-automatic and complete annotation of a chloroplast genome sequence, and the visualization, editing and analysis of the annotation results. It will become an indispensible tool for researchers studying chloroplast genomes. The software is freely accessible from http://www.herbalgenomics.org/cpgavas.
authors.affiliation: Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, 151 MaLianWa North Road, Haidian District, Beijing 100191, People's Republic of China. cliu@implad.ac.cn
authors.forename: Chang
authors.initials: C
authors.lastname: Liu
authors.forename: Linchun
authors.initials: L
authors.lastname: Shi
authors.forename: Yingjie
authors.initials: Y
authors.lastname: Zhu
authors.forename: Haimei
authors.initials: H
authors.lastname: Chen
authors.forename: Jianhui
authors.initials: J
authors.lastname: Zhang
authors.forename: Xiaohan
authors.initials: X
authors.lastname: Lin
authors.forename: Xiaojun
authors.initials: X
authors.lastname: Guan
mesh_terms: D030541:Databases, Genetic; D030561:Databases, Nucleic Acid; D054628:Genome, Chloroplast / Q000235:genetics*; D020407:Internet; D058977:Molecular Sequence Annotation / Q000379:methods*; D012984:Software; D013045:Species Specificity; D013223:Statistics as Topic / Q000379:methods*