Chloroplot

Chloroplot visualizes organelle genomes, with a focus on chloroplast genomes, producing scalable maps that depict gene features, Single Short Copy (SSC) and Inverted Repeat (IR) regions, and codon usage bias metrics for genes.

Key Features:

• SSC reverse-complement representation: Represents Single Short Copy (SSC) regions in reverse complement to facilitate depiction of codon usage bias index for each gene.
• Codon usage bias per gene: Depicts codon usage bias index at the gene level to support analysis of coding sequence characteristics.
• Inverted Repeat (IR) mismatch visualization: Visualizes minor mismatches between Inverted Repeat (IR) regions and plotting layers to highlight structural variation.
• Customizable color schemes and plotting functionalities: Provides diverse color schemes and plotting functionalities tailored to represent plastid genome features and differentiate genomic elements.
• Scalable genomic representation: Generates scalable representations of genomic content that allow adjustment of display detail across genome maps.

Scientific Applications:

• Plant genomics: Supports analysis of chloroplast genome structure and function in plant genomics research.
• Comparative genomics: Aids comparative analyses of plastid genomes by visualizing structural differences and gene-level metrics.
• Evolutionary biology: Assists studies of genome evolution by highlighting IR mismatches and other structural variations.
• Functional genomics: Facilitates investigation of codon usage bias and its potential implications for gene expression regulation.

Methodology:

Implemented in R using the Shiny framework.