iceLogo statistics

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Citations per year

Number of citations per year for the bioinformatics software tool iceLogo
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Tool usage distribution map

This map represents all the scientific publications referring to iceLogo per scientific context
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Protocols

iceLogo specifications

Information


Unique identifier OMICS_05885
Name iceLogo
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Java
License Apache License version 2.0
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


No version available

Maintainer


  • person_outline Lennart Martens

Information


Unique identifier OMICS_05885
Name iceLogo
Interface Web user interface
Restrictions to use None
Programming languages Java
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Lennart Martens

Publications for iceLogo

iceLogo citations

 (68)
library_books

SmSP2: A serine protease secreted by the blood fluke pathogen Schistosoma mansoni with anti hemostatic properties

2018
PLoS Negl Trop Dis
PMCID: 5931690
PMID: 29677188
DOI: 10.1371/journal.pntd.0006446

[…] on, peptide cleavage products with >10-fold change in peak area intensity and p-value <0.05 were identified and the peptide sequence corresponding to the P4 to P4' subsite positions were used to make IceLogo frequency plots []. Mass spectrometry data and results can be accessed here: ftp://massive.ucsd.edu/MSV000081747. […]

library_books

Substrate Specificity of Cysteine Proteases Beyond the S2 Pocket: Mutagenesis and Molecular Dynamics Investigation of Fasciola hepatica Cathepsins L

2018
Front Mol Biosci
PMCID: 5917446
PMID: 29725596
DOI: 10.3389/fmolb.2018.00040

[…] Protein Prospector score thresholds were set to 22 and 15 with maximum expectation values of 0.01 and 0.05 for protein and peptide matches, respectively. Peptide cleavage products were imported into iceLogo software v.1.2 to generate protease substrate specificity profiles (Colaert et al., ). Octapeptides (P4–P4′) corresponding to the peptide cleavage products were used as the positive dataset, a […]

library_books

N Terminomics TAILS Identifies Host Cell Substrates of Poliovirus and Coxsackievirus B3 3C Proteinases That Modulate Virus Infection

2018
J Virol
PMCID: 5874412
PMID: 29437971
DOI: 10.1128/JVI.02211-17

[…] used as a variable parameter. Carbamidomethylation (Cys) was used as a fixed modification in both searches, as well as variable methionine oxidation (+15.994915 Da).Sequence logos were generated with IceLogo with a P value of 5% (). Quadrupole time-of-flight (Q-TOF) data were similarly matched in MaxQuant, version 1.5.2.8, against a UniProt-derived murine proteome database (October 2013 release) w […]

library_books

Benchmarking common quantification strategies for large scale phosphoproteomics

2018
Nat Commun
PMCID: 5849679
PMID: 29535314
DOI: 10.1038/s41467-018-03309-6

[…] s from SAM testing (Fig. ). Where indicated, imputation was performed with the R package “impute” incorporated in the “samr” package using standard settings. Sequence motif logos were generated using iceLogo v1.2 with fold-change as the scoring system and a p-value cut-off of 0.05. Our input data sets were sequence windows for SAM upregulated phosphorylation sites of each quantification method. Fo […]

call_split

High throughput protease profiling comprehensively defines active site specificity for thrombin and ADAMTS13

2018
Sci Rep
PMCID: 5809430
PMID: 29434246
DOI: 10.1038/s41598-018-21021-9
call_split See protocol

[…] both enrichment and depletion. All significantly enriched and depleted peptides from the selections are available as supplemental files. Amino acid frequency plots and heatmaps were created using the iceLogo package, where the ratio of amino acid frequencies in the enriched peptides was compared to depleted peptides. In the case of thrombin, all peptides containing a single Arg were aligned and ce […]

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

[…] s. Hydrophobicity scores were calculated online with https://www.protpi.ch/Calculator. Their significance levels of control and IFNγ treated samples were calculated using a two-sided unpaired t test. IceLogo was used to calculate the statistics to find over-represented a.a. in each position of HLA-B*07:02, -A*68:01 and -A*03:01 predicted binders of the IFNγ dataset compared with the control, with […]


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iceLogo institution(s)
Department of Medical Protein Research, VIB, Ghent, Belgium; Department of Biochemistry, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
iceLogo funding source(s)
Ghent University [BOF12/GOA/014]; IWT SBO Grant ‘INSPECTOR’ [120025]

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