ggmotif

ggmotif extracts and visualizes sequence motifs from MEME (Multiple EM for Motif Elicitation) .xml and .txt outputs to support motif interpretation, sequence-logo generation, and integration with phylogenetic analyses.

Key Features:

• Motif Extraction: Parses MEME .xml and .txt outputs to extract motif definitions, motif occurrences, and precise motif locations within corresponding sequences.
• Visualization: Converts extracted motif data into R graphics for graphical representation of motifs.
• Integration with Phylogenetic Data: Maps motif occurrences onto phylogenetic trees via interoperability with the ggtree package.
• Sequence Logo Generation: Extracts sequences for identified motifs from .txt files and generates sequence logos using the ggseqlogo function from the ggseqlogo R package.

Scientific Applications:

• Genomics: Characterizing DNA regulatory motifs to inform studies of gene regulation.
• Proteomics: Analyzing protein sequence motifs to support inference of protein functional regions.
• Evolutionary Biology: Comparative motif analysis and visualization integrated with phylogenies to investigate evolutionary relationships.

Methodology:

Parses MEME-generated .xml and .txt files to extract motif information (definitions, locations, sequences), converts the data into formats for visualization and integration, generates sequence logos via ggseqlogo, and enables mapping of motifs to phylogenetic trees with ggtree within the R environment.