Predector

Predector predicts transcription factor binding sites and regulons in annotated bacterial genomes using position weight matrices (PWMs) to identify potential target genes.

Key Features:

• PWM-based prediction and scoring: Uses position weight matrices to scan annotated bacterial genomes and score candidate transcription factor binding sites.
• Positioning of sites: Reports genomic positions of predicted binding sites relative to annotated genes.
• Threshold estimation: Estimates score thresholds to help distinguish higher-confidence target genes from lower-confidence candidates.
• Search interval specification: Allows restriction of searches to intervals specified relative to gene start positions for cis-element detection.

Scientific Applications:

• Microbial genomics and systems biology: Supports identification of regulatory elements and integration into systems-level analyses of bacterial genomes.
• Regulatory network reconstruction: Facilitates prediction of transcription factor regulons for modeling regulatory networks.
• Gene regulation analysis: Identifies potential target genes and cis-regulatory elements to study transcriptional control mechanisms.
• Antibiotic resistance research, metabolic engineering and synthetic biology: Enables investigation of regulatory mechanisms relevant to antibiotic resistance and the design or modification of metabolic and synthetic pathways.

Methodology:

Uses position weight matrices (PWMs) to predict and score binding sites across annotated bacterial genomes, estimates score thresholds to prioritize targets, and supports searches limited to intervals relative to gene start positions.