STREME

STREME identifies novel sequence motifs in DNA, RNA, and protein sequences to detect biologically relevant patterns such as binding sites.

Key Features:

• Algorithmic performance: Outperforms DREME, HOMER, MEME, Peak-motifs, ProSampler, and Weeder and accurately identifies motifs from in vivo DNA (ChIP-seq) and RNA (CLIP-seq) data validated against in vitro reference motifs.
• Large-scale capability: Handles datasets containing hundreds of thousands of sequences.
• Motif length range: Discovers short and long motifs ranging from 3 to 30 positions.
• Alphabet support: Operates on DNA, RNA, protein, and user-defined alphabets.
• Differential motif discovery: Supports comparative motif discovery between pairs of sequence datasets to identify condition-specific differences.
• Statistical significance: Provides an estimate of statistical significance for each discovered motif.
• Integration: Integrated with the MEME Suite for incorporation into broader sequence analysis workflows.

Scientific Applications:

• Binding site discovery: Identification of DNA- and RNA-binding protein motifs to study regulatory interactions.
• In vivo dataset analysis: Extraction of motifs from ChIP-seq and CLIP-seq experiments.
• Benchmarking and validation: Comparison and validation of discovered motifs against in vitro reference motifs.
• Comparative studies: Differential motif analysis to detect motif changes across conditions or sample groups.

Methodology:

Performs ab initio motif discovery using probabilistic and discrete models and computes statistical significance estimates for discovered motifs.