IRscope

IRscope visualizes junction sites between inverted repeats and short and long single copy regions in chloroplast genomes to analyze and compare their structural organization.

Key Features:

• Visualization Capabilities: Depicts up to ten chloroplast genomes simultaneously to support comparative visualization of junction regions.
• Genomic Focus: Specifically targets the junction sites connecting inverted repeats to short and long single copy regions within chloroplast genomes.
• Scalability: Produces visual outputs scaled to reflect nucleotide base pair lengths in the vicinity of junction sites.
• Software Environment: Implemented in R for computation and visualization.
• Validation: Tested on over 100 embryophyte chloroplast genomes with consistent output generation.

Scientific Applications:

• Genomic Structure Analysis: Facilitates analysis of the structural organization and evolutionary dynamics of chloroplast IR/SC junctions.
• Comparative Genomics: Enables comparison of conserved and variable features across multiple chloroplast genomes.

Methodology:

Accepts GenBank (.gb) files, accession or GI numbers, and DOGMA output files as input.