WebLogo protocols

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

 (123)
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 omega50 and the consensus sequence logo was plotted using weblogo351. 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: 5780849
PMID: 29363428
DOI: 10.1186/s12864-017-4374-2

[…] the profile of up- and down-stream sequences (15 bases on each side) flanking editing sites using bedtools getfasta [53]; 2) visualizing the sequence context around rna editing sites using weblogo 3(weblogo –a dna –c classic –units probability –first-index −10) [54]., level of expressed genes in rpkm (reads per kilobase per million mapped reads) was estimated from rna-seq mapping […]

2018
PMCID: 5832876
PMID: 29497070
DOI: 10.1038/s41598-018-22093-3

[…] (intron or exon). sequences surrounding the splice sites where the sl sequence was inserted were retrieved from genes using bedtools version 2.17.052 and visualized as sequence logos using the weblogo 3.0 software53. to investigate feature changes between the cis- and trans-spliced sites, we used a conservative approach that focused on a set of trans-spliced genes with at least one […]

2018
PMCID: 5836110
PMID: 29343515
DOI: 10.1074/jbc.RA117.001614

[…] was performed with clustal omega, setting the l. monocytogenes gtlb protein as a reference. the alignment was subsequently used to generate a sequence logo motif using the web-based application weblogo (81)., j.r., m.g.p., and a.g. conceptualization; j.r., m.g.p., and a.g. resources; j.r. and m.g.p. data curation; j.r., m.g.p., and a.g. formal analysis; j.r. and a.g. funding acquisition; […]

2018
PMCID: 5865037
PMID: 29426042
DOI: 10.1128/IAI.00622-17

[…] equipped with a ×63 objective., multiple alignments of dblβ domains known to bind icam-1 were made using muscle v.3.7 software (58), and sequence distance trees were made with mega software (59). a weblogo 3 sequence logo (60) of the icam-1-binding motif was generated based on alignment of the included dblβ_motif domains (table 3) with the consensus motif i(v/l)x3n(e)gg(p/a)xyx27gppx3h (15, […]

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

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