BlockLogo: Visualization of peptide and sequence motif conservation

Lars Rønn Olsen, Ulrich Johan Kudahl, Christian Simon, Jing Sun, Christian Schönbach, Ellis L. Reinherz, Guang Lan Zhang, Vladimir Brusic

    Research output: Contribution to journalJournal articleResearchpeer-review

    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/.
    Original languageEnglish
    JournalJournal of Immunological Methods
    Volume400-401
    Pages (from-to)37-44
    ISSN0022-1759
    DOIs
    Publication statusPublished - 2013

    Keywords

    • T-cell epitope
    • B-cell epitope
    • Protein–protein interaction
    • Block entropy
    • Sequence variability and conservation

    Cite this

    Olsen, L. R., Kudahl, U. J., Simon, C., Sun, J., Schönbach, C., Reinherz, E. L., ... Brusic, V. (2013). BlockLogo: Visualization of peptide and sequence motif conservation. Journal of Immunological Methods, 400-401, 37-44. https://doi.org/10.1016/j.jim.2013.08.014
    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.
    @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",
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    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

    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 articleResearchpeer-review

    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 -