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pLogo specifications

Information


Unique identifier OMICS_05887
Name pLogo
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Publication for pLogo

pLogo in publications

 (24)
PMCID: 5768985
PMID: 29376036
DOI: 10.3389/fcimb.2017.00537

[…] as “analyzed list” and the v. cholerae v52 proteome as “reference list.” to analyse sequence motifs surrounding acetylation sites, we used the tools motif-x (v. 1.2) (schwartz and gygi, ) and plogo (o'shea et al., ). a 21 amino acid sequence window was chosen, the compiled v. cholerae v52 proteome was used as background, and otherwise default settings were applied. homology models […]

PMCID: 5889215
PMID: 29547119
DOI: 10.7554/eLife.35190.025

[…] for phosphorylation by c-abl by generating a sequence probability logo based on sequences in the subset of peptides with high enrichment scores () (). we refer to this sequence logo as a ‘phospho-plogo diagram’. this logo reflects the probability of finding a particular amino acid at a specific position in a good substrate, relative the same residue- and position-specific probabilities […]

PMCID: 5579049
PMID: 28860605
DOI: 10.1038/s41598-017-09918-3

[…] networks based on known protein-protein interactions was performed using the string database (v 10.0), and figure layout was modified with cytoscape (v 3.3.0). motif analysis was performed using plogo. domain information to map acetylations within domains was retrieved from the uniprot database., , electronic supplementary material , supplementary information accompanies this paper […]

PMCID: 5515926
PMID: 28720874
DOI: 10.1038/s41598-017-06219-7

[…] the p8-p8′ sites. to identify common patterns among different mmp substrate-cleavage sites from both source and target domains, we subsequently rendered sequence-logo representations using the plogo program. as shown in fig. , even though the residue distribution clearly varied among different mmp substrate-cleavage sites, they still exhibited similar sequence patterns. remarkably, glycine […]

PMCID: 5461540
PMID: 28373298
DOI: 10.1074/mcp.M116.065490

[…] ± 6 residues relative to the target site. because 82% of sequences contained a target threonine, we used only these sequences in generating the consensus motif. the sequence logo was created using plogo () with a background of all human protein sequences., hela cells were grown to confluency and treated with 150 mm okadaic acid for 2.5 h. cells were harvested in pbs and the pellet […]


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pLogo institution(s)
Department of Physiology and Neurobiology, University of Connecticut, Storrs, CT, USA

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