MONKEY

MONKEY identifies conserved transcription factor binding sites in multispecies alignments of non-coding DNA using probabilistic models of transcription factor sequence specificity and evolutionary dynamics.

Key Features:

• Probabilistic Modeling: Uses probabilistic frameworks to model transcription factor sequence specificity and the evolution of binding sites across species.
• Likelihood Computation: Computes likelihoods that putative binding sites are conserved across species to evaluate conservation evidence.
• Statistical Significance Assignment: Assigns statistical significance to detected hits to distinguish likely functional sites from background.
• Evolutionary Distance Analysis: Analyzes how evolutionary distance between species influences the conservation and significance of transcription factor binding sites.

Scientific Applications:

• Conservation Studies: Identifies conserved regulatory elements in non-coding regions to study evolutionary constraints on regulatory sequences.
• Functional Genomics: Correlates sequence conservation of transcription factor binding sites with potential regulatory function.
• Comparative Genomics: Enables comparison of regulatory element conservation across species, for example within Saccharomyces.

Methodology:

Analyzes multispecies alignments using probabilistic models that account for transcription factor sequence specificity and evolutionary changes, computes likelihoods of conservation for putative binding sites, and assigns statistical significance to each detected site.