Stubb: a program for discovery and analysis of cis-regulatory modules

Area of Science:

• Bioinformatics
• Computational Biology
• Genomics

Background:

• Discovering transcription factor binding site clusters is crucial for identifying cis-regulatory modules that control gene expression.
• Previous work developed the Stubb program, a probabilistic and maximum likelihood method for efficient cis-regulatory module detection at genomic scales.
• Leveraging a second related genome can enhance the accuracy of module predictions.

Purpose of the Study:

• To present a novel web-based interface for the Stubb program.
• To facilitate the discovery and in-depth analysis of cis-regulatory modules and their constituent transcription factor binding sites.
• To provide a user-friendly platform for genomic-scale cis-regulatory element identification.

Main Methods:

• Development of a web server implementing the Stubb program.
• Integration of a specialized post-processing module for detailed analysis of predicted cis-regulatory modules.
• Utilizing probabilistic models and maximum likelihood estimation for binding site cluster detection.

Main Results:

• A functional web server (http://stubb.rockefeller.edu/) is now available for public use.
• The interface enables efficient detection of cis-regulatory modules across large genomic regions.
• The post-processing step allows for precise identification of individual transcription factor binding sites within identified modules.

Conclusions:

• The Stubb web server offers an accessible and powerful tool for bioinformatics research.
• It significantly aids in the identification and characterization of cis-regulatory modules and their binding sites.
• This tool advances the study of gene regulation by providing a scalable and user-friendly solution.