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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

Versioning


No version available

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 citations

 (7)
library_books

Discrimination Between Human Leukocyte Antigen Class I Bound and Co Purified HIV Derived Peptides in Immunopeptidomics Workflows

2018
Front Immunol
PMCID: 5946011
PMID: 29780384
DOI: 10.3389/fimmu.2018.00912

[…] g 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 were ex […]

library_books

Phosphoproteomic insights into processes influenced by the kinase like protein DIA1/C3orf58

2018
PeerJ
PMCID: 5896498
PMID: 29666759
DOI: 10.7717/peerj.4599

[…] , and 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 numbers […]

library_books

High throughput and Sensitive Immunopeptidomics Platform Reveals Profound Interferonγ Mediated Remodeling of the Human Leukocyte Antigen (HLA) Ligandome*

2017
PMCID: 5836376
PMID: 29242379
DOI: 10.1074/mcp.TIR117.000383

[…] Gibbscluster-2.0e () was run independently for each sample using all HLA-IIp identified in a given sample, with the default options except that the number of clusters was tested between 1 and 6, the n […]

library_books

GibbsCluster: unsupervised clustering and alignment of peptide sequences

2017
Nucleic Acids Res
PMCID: 5570237
PMID: 28407089
DOI: 10.1093/nar/gkx248

[…] ty if the motifs are located at different locations within the peptides (i.e. they require an alignment), or if they have heterogeneous length (i.e. they contain insertions or deletions (indels)).The GibbsCluster server was created to deal with the challenges mentioned above, aiding the identification of motifs in peptides datasets that are in general unaligned, consist of multiple specificities a […]

library_books

Direct identification of clinically relevant neoepitopes presented on native human melanoma tissue by mass spectrometry

2016
Nat Commun
PMCID: 5121339
PMID: 27869121
DOI: 10.1038/ncomms13404

[…] representative 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 from EN […]

library_books

Sampling From the Proteome to the Human Leukocyte Antigen DR (HLA DR) Ligandome Proceeds Via High Specificity*

2016
PMCID: 4824864
PMID: 26764012
DOI: 10.1074/mcp.M115.055780

[…] R11, 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 (), with preferenc […]


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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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