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GibbsCluster specifications

Information


Unique identifier OMICS_10006
Name GibbsCluster
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data All the input sequences must be in one-letter amino acid code.
Operating system Unix/Linux
Computer skills Advanced
Version 1.0
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Morten Nielsen <>

Information


Unique identifier OMICS_10006
Name GibbsCluster
Interface Web user interface
Restrictions to use None
Input data All the input sequences must be in one-letter amino acid code.
Computer skills Basic
Version 1.0
Stability Stable
Maintained Yes

Maintainer


  • person_outline Morten Nielsen <>

Publication for GibbsCluster

GibbsCluster in publications

 (6)
PMCID: 5946011
PMID: 29780384
DOI: 10.3389/fimmu.2018.00912

[…] the default settings for shannon type logos in seq2logo2.0 (). area-proportional venn diagrams were created using the online biovenn tool (). gibbs clustering analysis was performed with the online gibbscluster2.0 server using the default settings for mhc class i ligands with 1–5 clusters (). for comparison to mass spectrometry-acquired data, known peptide ligands for hla class i alleles […]

PMCID: 5896498
PMID: 29666759
DOI: 10.7717/peerj.4599

[…] networkin, which adds protein interaction information to improve netphorest predictions., the phosphositeplus database (, ) was used to relate the observed phosphosites to literature findings., the gibbscluster-2.0 server was applied for clustering of phosphosite sequences. the regions surrounding the phosphorylated residue were considered (plus–minus three residues), and several desired […]

PMCID: 5836376
PMID: 29242379
DOI: 10.1074/mcp.TIR117.000383

[…] to bind to only one hla allotype. the threshold for binding was set to rank <2% and the respective affinity values in nm were extracted. sequence motifs were calculated and visualized from gibbscluster-2.0e () and seq2logo (). for length distribution, affinity and hydrophobicity analyses, we enabled the option of “match between runs” only within the control and ifnγ groups and used […]

PMCID: 5121339
PMID: 27869121
DOI: 10.1038/ncomms13404

[…] allotypes were calculated for the taa-derived peptides using netmhccons, and are provided in . clustering of peptides into groups based on sequence similarities was performed using the gibbscluster-1.1 tool using default settings., for prediction of affinity scores of mutated peptide ligands, protein transcript sequences associated with non-synonymous mutations were downloaded […]

PMCID: 4824864
PMID: 26764012
DOI: 10.1074/mcp.M115.055780

[…] and hla-dr52 were predicted using the netmhpan-3.0 algorithm (). peptides with a moderate to high binding affinity (ic) < 1000 nm were considered as potential binder for a particular allele. the gibbscluster-1.0 algorithm () was for simultaneous alignment and clustering of complete date set of hla-dr-associated peptides. gibbs clustering was performed using default settings (), […]


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GibbsCluster institution(s)
Center for Biological Sequence Analysis, Technical University of Denmark, DK Lyngby, Denmark
GibbsCluster funding source(s)
The research leading to these results received funding from the European Union Seventh Framework Program FP7/2007-2013 under grant agreement n° 222773).

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