Skylign protocols

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Skylign specifications

Information


Unique identifier OMICS_02182
Name Skylign
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Publication for Skylign

Skylign in pipelines

 (2)
2017
PMCID: 5702417
PMID: 29259976
DOI: 10.1155/2017/1728456

[…] script (distributed with fasttree). trees were visualized and annotated in dendroscope 3 []., sequence logos representing dna and protein sequence alignments were produced using skylign web server http://skylign.org []., nucleotide sequences were analyzed to assess both inter- and intrapatient quasispecies heterogeneity dynamics during the follow-up. sequences corresponding […]

2016
PMCID: 5100175
PMID: 27821048
DOI: 10.1186/s12864-016-3201-5

[…] the glpl []. for those rghs in which all four motifs could be easily identified, the amino acid sequences were extracted and compiled together. clustal omega [] was used to align the sequences and skylign [] was used to determine the consensus sequences for the four conserved motifs mentioned above. sequences that closely followed the consensus sequence for each motif were kept […]


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Skylign in publications

 (23)
PMCID: 5929573
PMID: 29672509
DOI: 10.1371/journal.pgen.1007357

[…] in one replicate of the wild type grown in rich medium using perl v5.18.2, followed by generation of a hidden markov model with the hmmbuild function of hmmer v3.1b2 [] and visualization with the skylign webserver []., putative orthologous proteins between species were identified with a blast-bbh approach, implemented using a modified version of our in-house shell and perl pipeline []. […]

PMCID: 5881046
PMID: 29427431
DOI: 10.1128/AEM.02773-17

[…] examples and may be important for the thermostability of these enzymes (, ). the alignment was used for the construction of a hidden markov model. for visualization, an hmm logo was created via the skylign online tool (http://skylign.org/; ). a subsequent visual analysis and conservation prediction using the js divergence scoring method revealed at least eight conserved regions ()., an initial […]

PMCID: 5851678
PMID: 29546243
DOI: 10.1126/sciadv.aap9714

[…] against the polyhistidine-tag (sigma)., a manually curated sequence alignment of the ef-tu superfamily was retrieved from the pfam database (). the pfam alignment was used as input for the program skylign () to generate logos representing the multiple sequence alignment and conservation of the superfamily. figure s11 shows logos illustrating the degree of conservation of each phosphorylation […]

PMCID: 5864071
PMID: 29529020
DOI: 10.1371/journal.pbio.2004328

[…] the major domain classes. domains identified using hmmer3 [] were grouped into their major domain classes and aligned using gismo []. sequence logos of the resulting alignments were generated using skylign [] (see ). gismo [] was found to handle the large diversity in the var domains better than other aligners. the resulting alignments were then segmented into regions of high and low occupancy. […]

PMCID: 5838249
PMID: 29507322
DOI: 10.1038/s41598-018-22441-3

[…] generated and calibrated using hmmer v3.0, on the basis of muscle protein alignments further edited with gblocks. logo representations of multiple protein sequence alignments were obtained using skylign. protein secondary structures for apicomplexan gna1 sequences were predicted using sable., prs421 vector (atcc 87475), containing ampicillin and met15, was modified by cloning s. cerevisiae […]


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Skylign institution(s)
HHMI Janelia Farm Research Campus, Ashburn, VA, USA

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