PredictRegulon

PredictRegulon predicts regulatory protein binding sites and operons in prokaryotic genomes by mapping known binding site alignments to upstream regions to identify cis-regulatory elements and downstream co-regulated genes.

Key Features:

• Input format: Accepts known or experimentally determined binding site sequences provided as ungapped multiple sequence alignments.
• Genome-wide upstream analysis: Systematically analyzes the upstream regions of all genes in a selected prokaryotic genome.
• Binding site prediction: Predicts potential regulatory protein binding sites within analyzed upstream regions.
• Operon identification: Identifies downstream co-regulated genes and candidate operons associated with predicted binding sites.
• Comparative discovery: Leverages known binding sites to discover orthologous binding sites in phylogenetically related genomes.
• Conservation analysis: Enables assessment of conservation of trans-acting regulator proteins and cognate cis-acting DNA sequences across species.

Scientific Applications:

• Regulatory annotation: Annotates cis-regulatory elements and candidate binding sites in prokaryotic genome sequences.
• Operon and regulon mapping: Identifies putative operons and co-regulated gene sets downstream of predicted binding sites.
• Comparative genomics: Detects orthologous regulatory sites in phylogenetically related genomes to study conservation of regulation.
• Functional genomics: Supports investigations into mechanisms of gene regulation by linking trans-acting regulators to cis-acting DNA sequences.

Methodology:

Accepts ungapped multiple sequence alignments of known binding sites, analyzes upstream regions of all genes in a selected prokaryotic genome to predict binding sites and identify downstream co-regulated genes (operons), and searches phylogenetically related genomes for orthologous binding sites.