PMScanR

PMScanR provides tools for large-scale protein motif analysis and visualization in R.

Key Features:

• Motif identification: Facilitates motif identification using external tools such as PROSITE's ps_scan, including handling necessary file downloads and execution.
• Output parsing: Parses scan outputs from external motif scanning tools.
• Format conversion: Converts scan outputs to GFF-like structures.
• Motif occurrence matrices: Generates motif occurrence matrices for downstream analysis.
• Visualization: Creates informative visualizations including heatmaps and sequence logos via seqLogo and ggseqlogo.

Scientific Applications:

• Protein motif analysis: Enables large-scale identification and exploration of motif patterns across multiple protein sequences.
• Downstream analysis: Supports downstream analysis of motif scanning results including statistical and comparative analyses.

Methodology:

PMScanR integrates with PROSITE's ps_scan for motif identification, parses the resulting scan outputs, and performs format conversion, matrix generation, and visualization using seqLogo and ggseqlogo.