RegPredict

RegPredict reconstructs microbial regulons and regulatory motif profiles using comparative genomics to identify co-regulated orthologous operons across prokaryotic genomes.

Key Features:

• Comparative genomics reconstruction: Reconstructs regulons across multiple prokaryotic genomes using comparative analysis of orthologous genes and operons.
• Cluster-based analysis: Groups co-regulated orthologous operons into clusters to distribute analysis of large regulons and enable independent comparative analyses of multiple clusters.
• Motif-driven workflow: Reconstructs regulons for known regulatory motifs using positional weight matrices.
• Ab initio regulon inference: Infers novel regulons ab initio by applying strategies to generate initial gene sets for downstream comparative analysis.
• Manually curated PWMs: Uses a collection of manually curated positional weight matrices of regulatory motifs for binding-site identification.
• Reference set generation: Produces reference sets of regulons and regulatory motif profiles across prokaryotic genomes.
• Data integration: Integrates genomic and functional information from multiple web resources to support regulon member characterization.
• Source data: Utilizes genomic sequences, ortholog predictions, and operon predictions obtained from MicrobesOnline.

Scientific Applications:

• Regulon reconstruction: Reconstructs regulatory networks for transcription factors with known motifs across prokaryotic genomes.
• Regulatory discovery: Identifies candidate novel regulons by ab initio inference from initial gene sets.
• Comparative analysis of regulatory networks: Enables cross-genome comparison of regulatory motifs and regulon composition using clustered orthologous operons.
• Reference motif profiling: Generates and refines reference regulatory motif profiles for use in binding-site prediction and comparative studies.

Methodology:

Comparative genomics using clusters of co-regulated orthologous operons; workflows for motif-driven regulon reconstruction and ab initio regulon inference from initial gene sets; application of manually curated positional weight matrices; and use of genomic sequences, ortholog predictions, and operon predictions from MicrobesOnline with integration of genomic and functional data from multiple web resources.