iCR

iCR predicts conserved regulatory binding sites and identifies conserved target orthologs across multiple prokaryotic genomes to support comparative analysis of gene regulation.

Key Features:

• Multiple Genome Analysis: Analyzes multiple prokaryotic genomes concurrently to detect conserved regulatory elements across related species.
• Conservation-Based Prediction: Leverages known binding sites provided as ungapped multiple sequence alignments to predict potential binding sites across genomes.
• Cluster of Orthologous Group (COG) Utilization: Employs COG indices to identify conserved target orthologs among predicted regulated genes.
• Functional Classification: Assigns Functional Class Codes based on COG classification for proteins encoded by downstream genes.

Scientific Applications:

• Comparative regulatory genomics: Identify gene regulatory circuits conserved across prokaryotic species.
• Evolutionary biology: Infer shared regulatory mechanisms through conservation of binding sites and orthologous targets.
• Functional genomics: Predict impacts of regulators on downstream operons and annotate putative regulatory targets with COG-based functions.
• Gene function and network hypothesis generation: Provide candidate co-regulated genes and operons for experimental follow-up in prokaryotic systems.

Methodology:

Analyzes upstream regions of genes using user-provided known or experimentally determined binding sequences supplied as ungapped multiple sequence alignments, compares predicted sites across selected prokaryotic genomes to identify conserved regulatory elements, and uses COG indices to identify conserved orthologous targets and assign Functional Class Codes.