Genome Surveyor

Genome Surveyor predicts transcription factor binding sites and discovers cis-regulatory modules (enhancers) in Drosophila by integrating motif-based predictions with phylogenetic information to study regulatory element conservation and function.

Key Features:

• GBrowse integration: Implemented on the GBrowse genome browser framework to support genome-scale integration of motif and CRM predictions.
• Transcription Factor Binding Prediction: Predicts TF binding targets using motifs that represent experimentally determined DNA binding specificities.
• Cis-Regulatory Module Discovery: Employs a technique for discovering cis-regulatory modules (CRMs, enhancers) that control spatial and temporal gene expression.
• Enhanced Motif Database: Expands supported motifs from approximately 100 to about 400 motifs to increase the breadth of TF binding predictions.
• Phylogenetic Averaging of Motif Scores: Implements phylogenetic averaging of motif scores across multiple species to incorporate evolutionary conservation into predictions.
• Evolutionary Comparison Across Species: Supports comparative analyses across an expanded set of Drosophila species, increasing coverage from two to twelve species.

Scientific Applications:

• Transcriptional regulation: Identifies TF binding sites and CRMs to elucidate mechanisms of transcriptional control in Drosophila.
• Developmental biology: Maps regulatory elements that underlie spatial and temporal gene expression during development.
• Evolutionary biology: Enables comparative studies of regulatory element conservation and divergence across Drosophila species.
• Functional genomics: Provides annotations of candidate regulatory regions for downstream functional characterization.

Methodology:

Integrates motif-based predictions using experimentally determined DNA binding specificities with phylogenetic averaging of motif scores across multiple Drosophila species to identify candidate cis-regulatory modules.