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Protocols

CyBase specifications

Information


Unique identifier OMICS_20997
Name CyBase
Restrictions to use Academic or non-commercial use
Database management system MySQL
Community driven No
Data access File download, Browse
User data submission Not allowed
Maintained Yes

Subtools


  • Alpha Plot
  • Assays
  • Cyclic Seqplot
  • Cyclisation energy
  • cyclomod
  • Cyclotide Collier de Perles
  • cyclotide loop view
  • Cyclotide synthetic analogs
  • Cypred
  • Digest Peptide
  • Fingerprint Search
  • Primer Match
  • Sequence Diversity Wheel
  • Synthetic analogues
  • Termini Distance Distributions
  • Termini Proximity

Maintainer


  • person_outline David Craik

Publications for CyBase

CyBase citations

 (2)
library_books

Cyclotide Evolution: Insights from the Analyses of Their Precursor Sequences, Structures and Distribution in Violets (Viola)

2017
Front Plant Sci
PMCID: 5741643
PMID: 29326730
DOI: 10.3389/fpls.2017.02058

[…] The assembled transcriptomes were searched for similar sequences to the cyclotides from Cybase (cutoff date: 3.02.2014; http://www.cybase.org.au/) by the standalone NCBI-blast+ service (2.2.28) (tblastn, E-value cutoff: 50) in the Ugene software package (Okonechnikov et al., ). In parall […]

call_split

Peptidomics of Circular Cysteine Rich Plant Peptides: Analysis of the Diversity of Cyclotides from Viola tricolor by Transcriptome and Proteome Mining

2015
J Proteome Res
PMCID: 4642221
PMID: 26399495
DOI: 10.1021/acs.jproteome.5b00681
call_split See protocol

[…] p-project (www.onekp.com). BLAST searches were conducted against these scaffolds. The V. tricolor data were accessed via tBLASTn using a set of published cyclotide precursor sequences as queries (www.cybase.org.au). Resulting hits and contig sequences were translated and annotated based on homology to known cyclotide precursors according to a similar methodology as described recently. Briefly, hit […]


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CyBase institution(s)
Institute for Molecular Bioscience, Australian Research Council Special Research, Centre for Functional and Applied Genomics, University of Queensland, Brisbane, QLD, Australia; Université de Montpellier, CNRS, UMR5048, Centre de Biochimie Structurale, Montpellier, France

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