CpGAVAS, an integrated web server for the annotation, visualization, analysis, and GenBank submission of completely sequenced chloroplast genome sequences

By Chang Liu, Linchun Shi, Yingjie Zhu, Haimei Chen, Jianhui Zhang, Xiaohan Lin, Xiaojun Guan. BMC Genomics, 2012

590 citations recorded by the source corpus.

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. 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. 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 fromhttp://www.herbalgenomics.org/cpgavas.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/119e695b1aee81b9d65497cb633b63d58d71d0a2

How researchers see this paper

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In Molecular Biology

1. Stephan Greiner
2. Pascal Lehwark
3. Ralph Bock
4. Chang Liu
5. Haimei Chen
6. Linchun Shi

Citations in the corpus

• GeSeq – versatile and accurate annotation of organelle genomes (2017, background): “Mitofy (2) was developed for the annotation of plant mitochondrial sequences only, whereas CpGAVAS (3) and Verdant (4) solely annotate chloroplast genomes.”
• CPGAVAS2, an integrated plastome sequence annotator and analyzer (2019, methodology): “The first part was optimized based on the pipelines implemented in CPGAVAS (3).”
• OrganellarGenomeDRAW (OGDRAW) version 1.3.1: expanded toolkit for the graphical visualization of organellar genomes (2019, background): “, GetOrganelle or IOGA; (4,5)], and we are currently aware of no less than twelve (semi-)automatic annotation tools for organellar genomes (1,3,6-15).”
• CPGView: A package for visualizing detailed chloroplast genome structures (2023, methodology): “However, only CPGAVAS2 can generate a circular map with repeat distribution.”