Sybil protocols

View Sybil computational protocol

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Sybil specifications

Information


Unique identifier OMICS_00945
Name Sybil
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline David R. Riley <>

Publications for Sybil

Sybil in pipelines

 (11)
2017
PMCID: 5372535
PMID: 28264491
DOI: 10.3390/ijms18030519

[…] in each genome. gene prediction was performed with glimmer v.3.0.2 [] and hand-curated. comparison of the genetic regions was performed using the clovr comparative pipeline [] and explored using sybil []., the predicted protein sequence of one arbitrarily selected o-antigen ligase from each wa region 1 genomic organization was retrieved and aligned with muscle []. prediction […]

2017
PMCID: 5620648
PMID: 28895889
DOI: 10.3390/microorganisms5030057

[…] the genomic context of the hyl gene, we used sybil []. the sybil database for p. acnes was established and described previously [] and is accessible here: http://sybil-clovr.igs.umaryland.edu/sybil/christianscholz_pacnes_sybil., total rna from p. acnes (kpa171202 (type ib), and 12.1.l1 (type ia)) grown under anaerobic conditions to the exponential and stationary growth phase in bhi medium […]

2016
PMCID: 4938664
PMID: 27194801
DOI: 10.1534/g3.116.028449

[…] set. wau was not included in previous analyses because it was published after cog assessment was completed. the wmel genes were classified as either: 1) having an ortholog in wtpre (as determined by sybil cog assessment), 2) being truncated in wtpre (as determined by the homolog of a truncated wtpre gene sharing cog membership with the respective wmel gene), or 3) absent in wtpre., the t. […]

2016
PMCID: 4938664
PMID: 27194801
DOI: 10.1534/g3.116.028449

[…] ) were used in comparative analyses. previously published genomes were reannotated with the igs annotation engine, and clusters of orthologous genes (cogs) across all 18 genomes were defined using sybil (http://sybil.sourceforge.net/index.html, ; ). genome completeness was assessed with the busco pipeline () using the 40 core bacterial genes from compared to the gene set from each wolbachia […]

2016
PMCID: 4961843
PMID: 27447865
DOI: 10.1038/ncomms12218

[…] relies on an all-vs-all blastp search of the 19 genomes' predicted proteins, and the default parameters were used throughout. the resulting clusters and their genomic context were then examined with sybil, a web-based software package whose primary aim is to facilitate the analysis and visualization of comparative genome data, with a particular emphasis on protein and gene cluster data., […]


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Sybil in publications

 (19)
PMCID: 5736797
PMID: 29109175
DOI: 10.1128/IAI.00612-17

[…] from the two strains grown under sr and non-sr conditions were normalized for read numbers. orthologous genes shared by the two strains were identified using the clovr-comparative pipeline (, ) and sybil (). normalized read counts for orthologs were compared directly using in-house scripts., fifty-milliliter cultures of gbs were grown in tsb or new granada medium with appropriate selection […]

PMCID: 5723337
PMID: 29259589
DOI: 10.3389/fmicb.2017.02389

[…] ) against m. bovis and m. tuberculosis genomes., for the identification of groups of orthologous proteins among virulent m. bovis, m. bovis bcg, and m. tuberculosis, all genomes were analyzed using sybil, a comparative genomics platform provided by the institute for genome sciences, university of maryland, usa. sybil and associated algorithms identified protein clusters using reciprocal best […]

PMCID: 5620648
PMID: 28895889
DOI: 10.3390/microorganisms5030057

[…] reference sequence []. sequence alignment and phylogeny were done in mega 6.06, using muscle and minimum-evolution algorithms, respectively. to compare the genomic context of the hyl gene, we used sybil []. the sybil database for p. acnes was established and described previously [] and is accessible here: http://sybil-clovr.igs.umaryland.edu/sybil/christianscholz_pacnes_sybil., total rna […]

PMCID: 5372535
PMID: 28264491
DOI: 10.3390/ijms18030519

[…] in each genome. gene prediction was performed with glimmer v.3.0.2 [] and hand-curated. comparison of the genetic regions was performed using the clovr comparative pipeline [] and explored using sybil []., the predicted protein sequence of one arbitrarily selected o-antigen ligase from each wa region 1 genomic organization was retrieved and aligned with muscle []. prediction […]

PMCID: 5106034
PMID: 27835655
DOI: 10.1371/journal.pone.0165755

[…] glutamine and glycine were selected, blosum for proteins was used as matrix. synteny of genomic regions around the anafp locus in the genomes of the genus aspergillus was analyzed using the sybil algorithm [] at aspgd (www.aspgd.com) []., retentostat cultivation of strain pk1.22 (panafp::eyfp, δanafp) was performed according to []. in brief, continuous cultivation was started […]


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Sybil institution(s)
Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA; Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, USA
Sybil funding source(s)
Platform for Appropriate Technology in Health (PATH) Contracts (GAT.0782-01990-COA and 003024)

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