BlockLogo

BlockLogo visualizes and analyzes protein and nucleotide sequence motifs by computing block entropy from multiple sequence alignments to represent continuous and discontinuous motifs.

Key Features:

• Block entropy calculations: Computes block entropy from multiple sequence alignments to quantify information content of continuous and discontinuous motifs.
• Alignment input and selection: Processes multiple sequence alignments and permits selection of specific motif positions and sequence type (protein or nucleotide).
• Output formats: Produces BlockLogos, traditional sequence logos, and tables of motif frequencies.
• Discontinuous motif representation: Visualizes discontinuous motifs composed of non-adjacent positions and represents motifs in compact form often using regular expressions.
• MHC binding prediction integration: Integrates experimentally validated prediction algorithms to generate real-time MHC binding affinity predictions for 15 common HLA class I and II alleles.
• HLA-DR specificity analysis: Analyzes structural motifs that influence peptide binding specificity to HLA-DR molecules.

Scientific Applications:

• Epitope visualization: Visualizing T-cell and B-cell epitopes, including both continuous and discontinuous motifs.
• Peptide–MHC interaction studies: Investigating peptide–MHC interactions and predicting MHC binding affinities for immune-response studies.
• Structural motif characterization: Characterizing structural and functional motifs that affect peptide binding and protein interactions.
• Discontinuous epitope analysis: Performing visual analyses of discontinuous epitopes derived from multiple sequence alignments.

Methodology:

Computes block entropy from multiple sequence alignments and integrates experimentally validated MHC binding prediction algorithms to generate real-time binding affinity predictions for 15 common HLA class I and II alleles.