BlockLogo: Visualization of peptide and sequence motif conservation

Research output: Contribution to journalJournal article – Annual report year: 2013Researchpeer-review

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BlockLogo: Visualization of peptide and sequence motif conservation. / Olsen, Lars Rønn; Kudahl, Ulrich Johan; Simon, Christian; Sun, Jing; Schönbach, Christian; Reinherz, Ellis L.; Zhang, Guang Lan; Brusic, Vladimir.

In: Journal of Immunological Methods, Vol. 400-401, 2013, p. 37-44.

Research output: Contribution to journalJournal article – Annual report year: 2013Researchpeer-review

Harvard

Olsen, LR, Kudahl, UJ, Simon, C, Sun, J, Schönbach, C, Reinherz, EL, Zhang, GL & Brusic, V 2013, 'BlockLogo: Visualization of peptide and sequence motif conservation', Journal of Immunological Methods, vol. 400-401, pp. 37-44. https://doi.org/10.1016/j.jim.2013.08.014

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Author

Olsen, Lars Rønn ; Kudahl, Ulrich Johan ; Simon, Christian ; Sun, Jing ; Schönbach, Christian ; Reinherz, Ellis L. ; Zhang, Guang Lan ; Brusic, Vladimir. / BlockLogo: Visualization of peptide and sequence motif conservation. In: Journal of Immunological Methods. 2013 ; Vol. 400-401. pp. 37-44.

Bibtex

@article{628b1a95a2434a29be7e8c67e5c3fa7c,
title = "BlockLogo: Visualization of peptide and sequence motif conservation",
abstract = "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/.",
keywords = "T-cell epitope, B-cell epitope, Protein–protein interaction, Block entropy, Sequence variability and conservation",
author = "Olsen, {Lars R{\o}nn} and Kudahl, {Ulrich Johan} and Christian Simon and Jing Sun and Christian Sch{\"o}nbach and Reinherz, {Ellis L.} and Zhang, {Guang Lan} and Vladimir Brusic",
year = "2013",
doi = "10.1016/j.jim.2013.08.014",
language = "English",
volume = "400-401",
pages = "37--44",
journal = "Journal of Immunological Methods",
issn = "0022-1759",
publisher = "Elsevier",

}

RIS

TY - JOUR

T1 - BlockLogo: 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

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 - T-cell epitope

KW - B-cell epitope

KW - Protein–protein interaction

KW - Block entropy

KW - Sequence variability and conservation

U2 - 10.1016/j.jim.2013.08.014

DO - 10.1016/j.jim.2013.08.014

M3 - Journal article

VL - 400-401

SP - 37

EP - 44

JO - Journal of Immunological Methods

JF - Journal of Immunological Methods

SN - 0022-1759

ER -