WebLogo protocols

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WebLogo specifications

Information


Unique identifier OMICS_05886
Name WebLogo
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

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Maintainer


  • person_outline WebLogo Team <>

Information


Unique identifier OMICS_05886
Name WebLogo
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline WebLogo Team <>

Publication for WebLogo

WebLogo in pipelines

 (198)
2018
PMCID: 5777986
PMID: 29358647
DOI: 10.1038/s41598-018-19640-3

[…] after removing incomplete entries, 3120 sequences were obtained. among them, the 111 enterobacterial homologues were aligned with clustal omega and the consensus sequence logo was plotted using weblogo3. the degree of sequence similarity of tat proteins between e. coli (tata, tate, tatb) and c. glutamicum (tata, tate, tatb) or b. subtilis (tatay, tatac, tatad) were investigated […]

2018
PMCID: 5780444
PMID: 29403457
DOI: 10.3389/fmicb.2018.00002

[…] sequences were predicted using bprom with default parameters. the promoter sequences were aligned separately for each motif (-10 box and -35 box) using clustalw (). logos were prepared using weblogo ()., rna-seq results were verified using quantitative reverse-transcription polymerase chain reaction (qrt-pcr) analysis of host (siga, rnpb) and phage genes (gp005, gp054, gp062, gp087, […]

2018
PMCID: 5785536
PMID: 29371626
DOI: 10.1038/s41467-017-02342-1

[…] of 1.4. for each of the three largest clusters, protein sequences were aligned using mafft 7.31 and positions with more than 50% of gaps were discarded. logo consensus sequences were created using weblogo 3 program. transmembrane helices were predicted using tmhmm server 2.05 on the consensus sequences. global phylogenetic tree was constructed from a global alignment using mafft 7.310. […]

2018
PMCID: 5816076
PMID: 29483897
DOI: 10.3389/fmicb.2018.00046

[…] (lefort et al., ). the itol suite was used to generate graphical representation of phylogenetic trees (letunic and bork, ). sequence consensus motifs were represented as logos, obtained at the weblogo website (http://weblogo.berkeley.edu/; schneider and stephens, ; crooks et al., )., synthetic genes encoding cdpss 62-103 and optimized for expression in e. coli were obtained from geneart. […]

2018
PMCID: 5818608
PMID: 29459752
DOI: 10.1038/s41598-018-21190-7

[…] in introns by searching regions relative to the 3′ splicing site, using an in house perl script. sequence logos of all detected junctions and junctions with coverage depth ≥ 3 were generated by weblogo and consensus sequences were generated by the tool cons from emboss, respectively. introns and splicing patterns were identified according to the letters on donor and acceptor sites […]


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WebLogo in publications

 (1510)
PMCID: 5945682
PMID: 29748556
DOI: 10.1038/s41467-018-04232-6

[…] sequences (nr) database using psi-blast (position-specific iterated blast) in ncbi. conserved amino acid residues were predicted from the top 1000 srpa homologous sequences using an online tool weblogo (http://weblogo.berkeley.edu/)., overnight culture of strain 1–9 was co-cultivated with serial dilutions of the phage k5 at mois of 0, 1, and 10, respectively. optical densities of cultures […]

PMCID: 5954277
PMID: 29764390
DOI: 10.1186/s12864-018-4469-4

[…] of the overlapping motifs was performed to check conserved bases by using the clustalw program (version 2.1) []. the sequence logos for consensus dna-binding sites were then displayed using the weblogo tool []., top10 3-mer and 4-mer motifs and sequence logos of each cstf on all other conditions can be retrieved from our online database (http://wcchang.itps.ncku.edu.tw/cstfanalysis/). […]

PMCID: 5943514
PMID: 29743536
DOI: 10.1038/s41598-018-25765-2

[…] mcpip1-triggered degradation of rna, we presented the identified sites of cleavage as a consensus logo (supplementary fig. ). for logotype preparation, we used the sequence logo generator software weblogo. we figured out that cleavage sites lacking g nts in the immediate vicinity of the cut site were preferable for mcpip1-induced cleavage (supplementary fig. )., observed at fig.  […]

PMCID: 5946033
PMID: 29780389
DOI: 10.3389/fimmu.2018.00937

[…] (), and the proportion of each splice site motifs gt-ag, gc-ag, at-ac, and others was evaluated by the number of junctional read counts. sequence logos of splice site motifs were generated by weblogo., both gene expression and as analyses were performed as in our previous study (). for gene expression analysis, the number of reads falling in the meta-gene, which was created by merging […]

PMCID: 5935748
PMID: 29728569
DOI: 10.1038/s41598-018-25349-0

[…] 4.11.0 tool (http://meme-suite.org/tools/meme), using default settings, except that the maximum width was 50, the minimum width was 6, and the maximum number of motifs to find was 10. the online weblogo3 platform (http://weblogo.threeplusone.com/) was used to create the sequence logo of the barley sbp domain. the genomic and cdna sequences of hvspls were analysed to predict the putative […]


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WebLogo institution(s)
Department of Plant and Microbial Biology, University of California, Berkeley, California, USA

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