LogoMotif

LogoMotif catalogs characterized and predicted transcription factor binding sites (TFBS) and supplies associated position weight matrices (PWMs) and hidden Markov models (HMMs) for regulatory analysis in Actinobacteria.

Key Features:

• Characterized and predicted TFBS: Includes both experimentally characterized and computationally predicted transcription factor binding sites (TFBS) for Actinobacteria.
• Position weight matrices (PWMs): Provides PWMs associated with TFBS for motif analysis.
• Hidden Markov models (HMMs): Provides HMMs associated with TFBS for motif representation.
• Genome-wide TFBS predictions in Streptomyces: Contains genome-wide predictions of TFBS locations specifically within Streptomyces model organisms.
• Curated regulatory interactions: Contains a curated collection of regulatory interactions within Actinobacteria that support binding site annotations.
• Regulatory network visualizations: Includes visual representations of regulatory networks linking transcription factors to their binding sites.

Scientific Applications:

• Modeling regulatory mechanisms: Supports analysis and modeling of transcriptional regulatory networks underlying multicellular development in Actinobacteria.
• Specialized metabolite and antibiotic regulation: Enables investigation of regulatory control over specialized metabolite production, including antibiotics.
• Genome mining guidance: Guides genome mining efforts by providing predicted binding sites to prioritize regulatory loci.
• Streptomyces regulatory mapping: Facilitates genome-wide mapping of TFBS in Streptomyces model organisms to study regulatory architecture.

Methodology:

Provides position weight matrices (PWMs) and hidden Markov models (HMMs) linked to characterized and predicted TFBS, performs genome-wide TFBS predictions in Streptomyces, and associates curated regulatory interactions with binding site annotations.