BlockLogo: Visualization of peptide and sequence motif conservation

• Published in: Journal of immunological methods 2013-12, Vol.400-401, p.37-44
• Main Authors: Olsen, Lars Rønn, Kudahl, Ulrich Johan, Simon, Christian, Sun, Jing, Schönbach, Christian, Reinherz, Ellis L., Zhang, Guang Lan, Brusic, Vladimir
• Format: Article
• Language: English
• Subjects: Algorithms; alleles; Amino Acid Motifs - genetics; Amino Acid Sequence; Antigens, Plant - genetics; Antigens, Plant - metabolism; B-cell epitope; B-lymphocytes; binding capacity; Block entropy; Conserved Sequence - immunology; entropy; epitopes; Epitopes, B-Lymphocyte - chemistry; Epitopes, B-Lymphocyte - genetics; Epitopes, B-Lymphocyte - immunology; Epitopes, T-Lymphocyte - chemistry; Epitopes, T-Lymphocyte - genetics; Epitopes, T-Lymphocyte - immunology; HLA-DRB1 Chains - metabolism; Humans; Molecular Sequence Data; Online Systems; Orthomyxoviridae - genetics; Orthomyxoviridae - immunology; Peptides - chemistry; Peptides - genetics; Peptides - immunology; prediction; Protein Binding; Protein Conformation; Protein–protein interaction; sequence alignment; Sequence Alignment - methods; Sequence Analysis, Protein - methods; Sequence variability and conservation; Software; T-cell epitope; T-lymphocytes; Viral Proteins - genetics; Viral Proteins - metabolism
• ISSN: 0022-1759; 1872-7905
• DOI: 10.1016/j.jim.2013.08.014

BlockLogo is a web-server application for the visualization of protein and nucleotide fragments, continuous protein sequence motifs, and discontinuous sequence motifs using calculation of block entropy from multiple sequence alignments. The user input consists of a multiple sequence alignment, selection of motif positions, type of sequence, and output format definition. The output has BlockLogo along with the sequence logo, and a table of motif frequencies. We deployed BlockLogo as an online application and have demonstrated its utility through examples that show visualization of T-cell epitopes and B-cell epitopes (both continuous and discontinuous). Our additional example shows a visualization and analysis of structural motifs that determine the specificity of peptide binding to HLA-DR molecules. The BlockLogo server also employs selected experimentally validated prediction algorithms to enable on-the-fly prediction of MHC binding affinity to 15 common HLA class I and class II alleles as well as visual analysis of discontinuous epitopes from multiple sequence alignments. It enables the visualization and analysis of structural and functional motifs that are usually described as regular expressions. It provides a compact view of discontinuous motifs composed of distant positions within biological sequences. BlockLogo is available at: http://research4.dfci.harvard.edu/cvc/blocklogo/ and http://met-hilab.bu.edu/blocklogo/. •We developed a tool for visualization of linear and non-linear immunological motifs.•Utility is demonstrated for neutralizing influenza B cell epitopes.•Utility is demonstrated for allergenic and hypoallergenic Bet v 1 allergens.•Utility is demonstrated for variability of HLA-DRB1 binding pocket P1.•The BlockLogo tool is available at http://research4.dfci.harvard.edu/cvc/blocklogo/.