CpGAVAS

CpGAVAS annotates, visualizes, and analyzes complete chloroplast genome sequences generated by next-generation sequencing and prepares Sequin files for GenBank submission to support chloroplast genomic and evolutionary analyses.

Key Features:

• Genome Annotation: Accepts a complete chloroplast genome sequence and predicts protein-coding and rRNA genes by identifying and mapping full-length protein, cDNA, and rRNA sequences using integrated results from Blastx, Blastn, protein2genome, and est2genome, while tRNA genes are identified with tRNAscan and inverted repeats are detected with ARAGORN and vmatch.
• Summary Statistics: Calculates summary statistics for the annotated chloroplast genome to provide quantitative descriptions of genomic features and composition.
• Visualization: Generates a circular map of the chloroplast genome for visual representation of annotations.
• GenBank Submission: Creates a Sequin file to enable direct submission of annotated sequences to GenBank.
• Sequence Extraction: Extracts protein and mRNA sequences for specified genes and species from the annotated genome.
• Annotation Editing and Re-analysis: Produces annotation results in GFF3 format that can be edited and re-uploaded for updates and re-analysis.

Scientific Applications:

• Chloroplast genome annotation and analysis: Supports semi-automatic and complete annotation workflows, visualization, editing, and downstream analyses of chloroplast genomes.
• Evolutionary biology: Facilitates studies of species evolutionary history using annotated chloroplast genome sequences.

Methodology:

Accepts complete chloroplast genome sequences; predicts protein-coding and rRNA genes by mapping full-length protein, cDNA, and rRNA sequences using integrated Blastx, Blastn, protein2genome, and est2genome results; identifies tRNA genes with tRNAscan; detects inverted repeats with ARAGORN and vmatch; outputs annotations in GFF3, generates circular maps, creates Sequin files for GenBank submission, extracts protein and mRNA sequences, calculates summary statistics, and accepts edited GFF3 files for re-analysis.