R-chie

R-chie visualizes nucleic acid interactions and generates arc diagrams to represent RNA secondary structures and genomic interactions for analysis of cis and trans RNA-RNA, RNA-DNA, and DNA-DNA relationships.

Key Features:

• Arc diagram generation: Creates arc diagrams for RNA secondary structures to compare and analyze overlapping structural features.
• Base-pair ranking and color-coding: Ranks and color-codes base pairs to highlight relative support or importance within interactions.
• Visualization of genomic interactions: Displays genomic interaction data to represent DNA-DNA and RNA-DNA contacts across loci.
• Evolutionary information integration: Incorporates multiple-sequence alignments to display evolutionary covariation and relatedness among sequences.
• Comparison of interaction datasets: Compares two alternative sets of interaction data to visualize differences between predicted or observed interactions.
• Quantitative data integration: Integrates quantitative evidence into visualizations to represent strength or confidence of interactions.

Scientific Applications:

• Trans RNA-RNA and RNA-DNA transcriptome interactions: Visualization and comparison of intermolecular transcriptome interactions among RNAs and between RNA and DNA.
• Trans DNA-DNA genome interactions: Visualization and analysis of genome-wide DNA-DNA contacts and their structural relationships.

Methodology:

Generates arc diagrams for RNA secondary structures, incorporates multiple-sequence alignments to indicate evolutionary covariation, ranks and color-codes base pairs, compares alternative interaction datasets, and integrates quantitative experimental and computational evidence into the visualizations.