UniprotR

UniprotR retrieves, parses, clusters, and visualizes protein data from UniProtKB and integrates annotations from resources such as SWISS-MODEL and STRING to support proteomics, functional annotation, and comparative genomics analyses.

Key Features:

• Data Retrieval: Retrieves comprehensive protein information from UniProtKB by accession number, including names and taxonomy.
• Data Clustering: Supports clustering of proteins based on primary gene names or chromosomal locations.
• Visualization Capabilities: Generates Gene Ontology (GO) diagrams, chromosomal location maps, protein scoring and status charts, protein interaction networks, sequence phylogenetic trees, and physicochemical property plots.
• Integration with Other Databases: Integrates data and annotations from external resources such as SWISS-MODEL and STRING.
• Output Formats: Produces summarized outputs as data frames, CSV files, and graphical figures.

Scientific Applications:

• Proteomics analysis: Enables retrieval and visualization of protein-centric data for proteomics investigations.
• Functional annotation: Supports assignment and exploration of protein functions using GO diagrams and integrated annotations.
• Comparative genomics: Facilitates comparative analyses through clustering by gene name or chromosomal location.
• Evolutionary analysis: Supports inference of evolutionary relationships using sequence phylogenetic trees.

Methodology:

Retrieves and parses proteomics data from UniProtKB and integrated databases, performs clustering by primary gene names or chromosomal locations, and generates graphical outputs within an R implementation.