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 language | English |
|---|---|
| Pages (from-to) | 37-44 |
| Number of pages | 8 |
| Journal | Journal of Immunological Methods |
| Volume | 400-401 |
| Issue number | 1 |
| DOIs | |
| Publication status | Published - Dec 31 2013 |
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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
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 journal › Article
}
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 - © 2013.
PY - 2013/12/31
Y1 - 2013/12/31
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 - Algorithms
KW - Amino Acid Motifs
KW - Amino Acid Sequence
KW - Antigens, Plant
KW - Conserved Sequence
KW - Epitopes, B-Lymphocyte
KW - Epitopes, T-Lymphocyte
KW - HLA-DRB1 Chains
KW - Humans
KW - Molecular Sequence Data
KW - Online Systems
KW - Orthomyxoviridae
KW - Peptides
KW - Protein Binding
KW - Protein Conformation
KW - Sequence Alignment
KW - Sequence Analysis, Protein
KW - Software
KW - Viral Proteins
UR - http://www.scopus.com/inward/record.url?scp=84888429223&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=84888429223&partnerID=8YFLogxK
U2 - 10.1016/j.jim.2013.08.014
DO - 10.1016/j.jim.2013.08.014
M3 - Article
VL - 400-401
SP - 37
EP - 44
JO - Journal of Immunological Methods
JF - Journal of Immunological Methods
SN - 0022-1759
IS - 1
ER -