UniPROBE

UniPROBE catalogs quantitative DNA-binding specificities of proteins and protein complexes using universal protein-binding microarray (PBM) data to characterize k-mer preferences and derive position weight matrices (PWMs) and sequence logos.

Key Features:

• Quantitative Binding Preferences: Provides binding affinity measurements for all possible nucleotide k-mers of a given length derived from universal PBM experiments.
• Position Weight Matrix (PWM) Representation: Includes PWMs for each protein or protein complex that represent positional nucleotide preferences within k-mers.
• Graphical Sequence Logo Representations: Provides sequence logos that visualize nucleotide distribution and relative information content across k-mer positions.
• Database Expansion and Enhancements: Content has been increased by over 130% and entries are annotated with UniPROBE accession numbers.
• Protein BLAST Tool Integration: Integrates a protein BLAST (blastp) to identify sequence matches within the database.

Scientific Applications:

• Functional Genomics: Use quantitative protein-DNA specificity data to infer gene regulatory mechanisms.
• Protein Engineering: Inform design and modification of proteins to alter DNA-binding specificities.
• Comparative Studies: Enable comparative analysis of protein sequences and their binding properties across proteins or species using integrated blastp.

Methodology:

UniPROBE employs universal PBM technology to measure binding affinities to nucleotide k-mers, quantifies those affinities to generate PWMs, and produces graphical sequence logos to represent binding specificity.