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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

 (64)
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

[…] by 3cpro., our two-prong tails approach to identify substrates of 3cpro of two enteroviruses was chosen to inventory distinct cleavage specificities and possibly identify common substrates. the icelogo analysis of the 3cpro cleavage sites suggests that 3cpro is capable of accepting a wider range of amino acids within its active site, therefore allowing for cleavage of a broader range […]

library_books

Benchmarking common quantification strategies for large scale phosphoproteomics

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

[…] 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. […]

library_books

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

[…] 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 […]

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

[…] 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, […]

library_books

T cell receptor β chains display abnormal shortening and repertoire sharing in type 1 diabetes

2017
Nat Commun
PMCID: 5702608
PMID: 29176645
DOI: 10.1038/s41467-017-01925-2

[…] in fig. ). the same approach was used to investigate which variables affect the frequency of jdels., analysis of amino acid usage in t1d-enriched versus hd-enriched clonotypes was performed using icelogo. icelogo builds on probability theory to visualize significant conserved sequence patterns in multiple peptide sequence alignments against background (reference) sequence sets […]

library_books

Lysine acetylome profiling uncovers novel histone deacetylase substrate proteins in Arabidopsis

2017
Mol Syst Biol
PMCID: 5658702
PMID: 29061669
DOI: 10.15252/msb.20177819

[…] score for modified peptides ≥ 6, acetyllysine site localization probability ≥ 0.75; contaminants removed., additionally, we analyzed the local sequence context around the acetylation sites using icelogo (maddelein et al, ) in combination with the arabidopsis tair10 database with all identified proteins as background reference (fig d). overall, negatively charged amino acids, […]


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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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