mmeta

mmeta aligns transcription factor (TF) maps across multiple promoter regions to identify conserved regulatory elements among orthologous or co-regulated genes even when nucleotide sequence conservation is lacking.

Key Features:

• Alignment of TF-Maps: Aligns TF-maps, i.e., predictions of transcription factor binding sites, using both identity and positional information within promoter sequences.
• Multiple Promoter Comparisons: Applies a progressive alignment paradigm to compare multiple promoters simultaneously and detect conserved regulatory elements across species.
• Detection of Non-Collinear Conservation Blocks: Identifies non-collinear conservation blocks within TF-map alignments that are often missed by nucleotide-based methods.
• Reduction of Signal/Noise Ratio: Focuses on functional TF binding sites rather than raw nucleotide sequences to reduce the signal-to-noise ratio in regulatory element detection.

Scientific Applications:

• Characterization of Promoter Regions: Characterizes promoter regions from multiple orthologous genes or co-regulated genes (e.g., microarray-derived) to reveal high-level regulatory conservation.
• Annotation of Regulatory Elements: Annotates potential transcription factor binding sites on sets of co-regulated genes derived from high-throughput expression experiments.

Methodology:

Uses a refined algorithm optimized and validated on a collection of human, mouse, chicken and zebrafish orthologous gene promoters, and optimized to detect regulatory conservation in promoter and 3'UTR regions.