PRMD

PRMD provides comprehensive annotations and analysis of RNA modifications, including N6-methyladenosine (m6A), across 20 plant species.

Key Features:

• Extensive Species Coverage: Contains RNA modification data across 20 plant species.
• RMlevelDiff: Compares RNA modification levels across conditions or species.
• RMplantVar: Analyzes variation in RNA modifications among plant species.
• RNAmodNet: Constructs and analyzes networks involving RNA modifications and associated proteins.
• Blast: Performs sequence alignment searches to identify homologous sequences and functional annotations.
• mRNAbrowse: Displays mRNA sequences with annotated RNA modification sites.
• RNAlollipop: Visualizes RNA modification sites in a graphical lollipop-style format.
• JBrowse: Provides a genome browser view for genomic regions annotated with RNA modifications.
• Integrative Genomics Viewer (IGV): Visualizes large-scale genomic and transcriptomic datasets including RNA modifications.

Scientific Applications:

• Functional analysis of RNA modifications: Investigation of roles of RNA modifications in physiological and pathological processes in plants, including effects on RNA structure and molecular interactions.
• Comparative analysis: Comparative studies of modification levels and variation across the 20 plant species.
• Network and interaction studies: Analysis of RNA modification–protein interaction networks using RNAmodNet.
• Annotation and visualization: Interpretation of modification sites in genomic and transcriptomic contexts using mRNAbrowse, RNAlollipop, JBrowse, and IGV.

Methodology:

Aggregation and annotation of RNA modification data across multiple plant species, and application of bioinformatics techniques to enable comparative analyses, network exploration, and visualization.