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Protocols

CyMoBase specifications

Information


Unique identifier OMICS_30194
Name CyMoBase
Alternative name Pfarao
Restrictions to use None
Community driven No
Data access Browse
User data submission Not allowed
Maintained Yes

Maintainer


  • person_outline Martin Kollmar

Publication for CyMoBase

CyMoBase citations

 (17)
library_books

Myosin repertoire expansion coincides with eukaryotic diversification in the Mesoproterozoic era

2017
BMC Evol Biol
PMCID: 5583752
PMID: 28870165
DOI: 10.1186/s12862-017-1056-2

[…] ture-guided multiple sequence alignment []. The work-flow for adding a new sequence was as follows: we first determined the closest myosin homolog with a BLASTP search against all myosins included in CyMoBase (updated on a regular basis), then pre-aligned the new sequence to the closest homolog using ClustalW [], and finally added the pre-aligned sequence to the multiple sequence alignment of all […]

library_books

Distribution and evolution of stable single α helices (SAH domains) in myosin motor proteins

2017
PLoS One
PMCID: 5378345
PMID: 28369123
DOI: 10.1371/journal.pone.0174639

[…] 7919 Myosin sequences were obtained from CyMoBase (www.cymobase.org, []), release 19th December 2016, and sorted by class and taxonomy. SAH-domain prediction was performed by querying the Waggawagga API []. The prediction provides an SAH-sco […]

library_books

Fine Tuning Motile Cilia and Flagella: Evolution of the Dynein Motor Proteins from Plants to Humans at High Resolution

2016
Mol Biol Evol
PMCID: 5100056
PMID: 27880711
DOI: 10.1093/molbev/msw213

[…] g of the dataset, even very short fragments of only 100 amino acids should be sufficient now for correctly grouping the dynein fragment into one of the established classes using the BLASTP service at CyMoBase. Thus, it is very unlikely that the orphan “Fragments” will group to one of the established 17 classes if their full-length sequences become available. Seven of the DHCs were termed pseudogen […]

library_books

Coordinated recruitment of Spir actin nucleators and myosin V motors to Rab11 vesicle membranes

2016
eLife
PMCID: 5021521
PMID: 27623148
DOI: 10.7554/eLife.17523.023

[…] a certain species, EST data from the NCBI EST database has been analyzed to help in the annotation process. All sequence-related data and references to genome sequencing centers are available through CyMoBase (http://www.cymobase.org). […]

library_books

Polyphyly of nuclear lamin genes indicates an early eukaryotic origin of the metazoan type intermediate filament proteins

2015
Sci Rep
PMCID: 4448529
PMID: 26024016
DOI: 10.1038/srep10652

[…] tive splice variants. The different splice forms were not considered independently in the analysis but in all cases the same splice forms were taken for homologous IFs. All sequences are available at CyMoBase ( www.cymobase.org). CyMoBase offers search and filter functions for the data, and provides many additional information such as GenBank ID’s, gene structure representations, previously used ( […]

library_books

Six Subgroups and Extensive Recent Duplications Characterize the Evolution of the Eukaryotic Tubulin Protein Family

2014
Genome Biol Evol
PMCID: 4202323
PMID: 25169981
DOI: 10.1093/gbe/evu187

[…] ta (names, corresponding species, GenBank ID's, alternative names, corresponding publications, domain predictions, and sequences) and references to genome sequencing centers are available through the CyMoBase (www.cymobase.org, last accessed September 5, 2014) (). […]

Citations

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CyMoBase institution(s)
Group Systems Biology of Motor Proteins, Department of NMR-based Structural Biology, Max-Planck-Institute for Biophysical Chemistry, Göttingen, Germany; Department of Biology and Biochemistry, The Milner Centre for Evolution, University of Bath, Bath, UK

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