iceLogo statistics

To access cutting-edge analytics on consensus tools, life science contexts and associated fields, you will need to subscribe to our premium service.

Subscribe
info

Citations per year

Citations chart
info

Popular tool citations

chevron_left Sequence logo generation chevron_right
Popular tools chart
info

Tool usage distribution map

Tool usage distribution map
info

Associated diseases

Associated diseases

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


Add your version

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 in publications

 (64)
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 […]

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. […]

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 […]

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, […]

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 […]


To access a full list of publications, you will need to upgrade to our premium service.

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]

iceLogo reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review iceLogo