TY - JOUR
T1 - BlockLogo
T2 - Visualization of peptide and sequence motif conservation
AU - Olsen, Lars Rønn
AU - Kudahl, Ulrich Johan
AU - Simon, Christian
AU - Sun, Jing
AU - Schönbach, Christian
AU - Reinherz, Ellis L.
AU - Zhang, Guang Lan
AU - Brusic, Vladimir
N1 - Funding Information:
LRO was funded by the Novo Nordisk Foundation ; UJK was funded by the Oticon Foundation ; C. Simon was funded by the Novo Scholarship Programme ; and GLZ, JS, VB, and ELR acknowledge funding from NIH grant U01 AI 90043 .
PY - 2013
Y1 - 2013
N2 - 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/.
AB - 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/.
KW - B-cell epitope
KW - Block entropy
KW - Protein-protein interaction
KW - Sequence variability and conservation
KW - T-cell epitope
UR - http://www.scopus.com/inward/record.url?scp=84888429223&partnerID=8YFLogxK
U2 - 10.1016/j.jim.2013.08.014
DO - 10.1016/j.jim.2013.08.014
M3 - Article
AN - SCOPUS:84888429223
SN - 0022-1759
VL - 400-401
SP - 37
EP - 44
JO - Journal of Immunological Methods
JF - Journal of Immunological Methods
IS - 1
ER -