XSTREME

XSTREME performs comprehensive de novo motif discovery and enrichment analysis in DNA, RNA, and protein sequences or any user-defined alphabets to identify and characterize sequence motifs across datasets.

Key Features:

• Supported sequence types: Operates on DNA, RNA, protein sequences, and any user-defined alphabets and supports both extensive and limited datasets.
• De novo motif discovery: Implements MEME and STREME algorithms for discovery of novel motifs.
• Motif enrichment analysis: Evaluates motif enrichment across any position within input sequences rather than assuming central enrichment.
• SEA algorithm: Uses the SEA algorithm for statistical motif enrichment analysis.
• Significance and visualization: Produces motif significance estimates and visualizations including positional distribution plots and histograms of motif matches per sequence.
• Integration: Integrates with the MEME Suite of sequence analysis tools.

Scientific Applications:

• Genomic studies: Identification and characterization of DNA sequence motifs in genomic datasets.
• Transcriptomics: Discovery and enrichment analysis of RNA motifs relevant to transcript regulation.
• Proteomics: Detection of protein sequence motifs for functional and structural studies.
• Regulatory and functional motif analysis: Investigation of sequence functionalities and regulatory mechanisms via motif discovery and enrichment.

Methodology:

Performs de novo motif discovery with MEME and STREME, assesses motif enrichment with the SEA algorithm across full sequence positions, computes motif significance estimates, and generates positional distribution and motif-match-count histograms.