CompareProspector

CompareProspector identifies regulatory sequence motifs in higher eukaryotes by biasing Gibbs sampling toward evolutionarily conserved noncoding regions through cross-species comparative genomics.

Key Features:

• Comparative Genomics Integration: Biases Gibbs sampling toward sequences conserved across multiple species to prioritize functional noncoding regulatory elements.
• Motif Prediction and Identification: Outputs putative motifs as position-specific probability matrices and reports individual sites and their locations within input sequences.
• Cross-Species Conservation Analysis: Detects motifs conserved across species and has identified transcription factor motifs such as Mef2, Myf, Srf, and Sp1 in human-muscle genes via human-mouse comparison.
• Discovery of Novel Regulatory Elements: Discovers novel motifs exemplified by recovery of an NFAT motif from CD28-stimulated T-cell genes.
• Performance and Efficacy: Demonstrates improved motif-finding performance relative to other programs by incorporating comparative-genomics biased sampling for eukaryotic regulatory element identification.

Scientific Applications:

• Gene Expression Studies: Identifies conserved regulatory motifs to aid interpretation of gene regulation across species.
• Functional Genomics: Pinpoints known and novel motifs to investigate regulatory element roles in biological processes.
• Evolutionary Biology: Enables exploration of evolutionary constraints on noncoding sequences through comparative analysis.

Methodology:

Extends BioProspector's Gibbs sampling approach by biasing sampling toward conserved regions identified via cross-species sequence comparisons and outputs position-specific probability matrices along with site coordinates.