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 journalArticle

16 Citations (Scopus)

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
Pages (from-to)37-44
Number of pages8
JournalJournal of Immunological Methods
Volume400-401
Issue number1
DOIs
Publication statusPublished - Dec 31 2013

Fingerprint

Sequence Alignment
Peptides
Position-Specific Scoring Matrices
B-Lymphocyte Epitopes
Amino Acid Motifs
T-Lymphocyte Epitopes
Entropy
HLA-DR Antigens
Epitopes
Nucleotides
Alleles
Proteins

Keywords

  • Algorithms
  • Amino Acid Motifs
  • Amino Acid Sequence
  • Antigens, Plant
  • Conserved Sequence
  • Epitopes, B-Lymphocyte
  • Epitopes, T-Lymphocyte
  • HLA-DRB1 Chains
  • Humans
  • Molecular Sequence Data
  • Online Systems
  • Orthomyxoviridae
  • Peptides
  • Protein Binding
  • Protein Conformation
  • Sequence Alignment
  • Sequence Analysis, Protein
  • Software
  • Viral Proteins

ASJC Scopus subject areas

  • Immunology
  • Immunology and Allergy

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(1), 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, No. 1, 31.12.2013, p. 37-44.

Research output: Contribution to journalArticle

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, no. 1, pp. 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, No. 1. pp. 37-44.
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AU - Schönbach, Christian

AU - Reinherz, Ellis L.

AU - Zhang, Guang Lan

AU - Brusic, Vladimir

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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/.

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