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Protocols

WormBase specifications

Information


Unique identifier OMICS_01664
Name WormBase
Restrictions to use None
Database management system Other
Community driven Yes
Data access File download, Browse, Application programming interface
User data submission Allowed
Version WS261
Maintained Yes
Wikipedia https://en.wikipedia.org/wiki/WormBase

Taxon


  • Invertebrates
    • Caenorhabditis elegans

Documentation


Maintainers


  • person_outline Kevin L. Howe
  • person_outline Raymond Lee
  • person_outline WormBase Team

Additional information


http://www.wormbase.org/about/userguide/for_users#3120--10

Publications for WormBase

WormBase citations

 (455)
library_books

Genome wide expert annotation of the epigenetic machinery of the plant parasitic nematodes Meloidogyne spp., with a focus on the asexually reproducing species

2018
BMC Genomics
PMCID: 5934874
PMID: 29724186
DOI: 10.1186/s12864-018-4686-x

[…] nd step, we created a repertory of known epigenetic factors and associated protein domains from the 6 model species. Basically, we recovered all known chromatin factors based on (i) Swiss-Prot [] and Wormbase [] annotations, (ii) epigenetic factors-specific databases such as Histone database [], ChromoHub [] and Histome [], and (iii) literature [–]. This dataset of epigenetic factors constituted t […]

library_books

Deciphering the molecular determinants of cholinergic anthelmintic sensitivity in nematodes: When novel functional validation approaches highlight major differences between the model Caenorhabditis elegans and parasitic species

2018
PLoS Pathog
PMCID: 5931475
PMID: 29719008
DOI: 10.1371/journal.ppat.1006996

[…] Using the C. elegans ACR-8 amino-acid sequence as a query, tBLASTn searches were performed against 68 nematode genomic databases available in WormBase-ParaSite (version 8; http://parasite.wormbase.org/) (). This revealed that acr-8 homologs are present in all the available genomes from the nematode species representing the Clades III, IV and V (20, 17 and 24 species, respectively). Str […]

library_books

Identification and characterization of the Fasciola hepatica sodium and chloride dependent taurine transporter

2018
PLoS Negl Trop Dis
PMCID: 5942844
PMID: 29702654
DOI: 10.1371/journal.pntd.0006428

[…] tabase published by Gasser et al. [] and full-length mRNA was obtained by applying RACE techniques (for see PCR amplification of cDNA and cloning). The genomic sequence was obtained from the database WormBase (https://parasite.wormbase.org) [] and is based on the published F. hepatica genome (PRJEB6687) [].We analyzed the expression of FhTauT in various life stages by searching the compilation of […]

library_books

Enhanced JBrowse plugins for epigenomics data visualization

2018
BMC Bioinformatics
PMCID: 5921565
PMID: 29699480
DOI: 10.1186/s12859-018-2160-z

[…] e these data sets effectively, hindering the visualization and potential discoveries with new sequencing technologies. JBrowse is used by numerous scientific resources, such as Phytozome [], CoGe [], WormBase [], and Araport [] because it is highly customizable and adaptable with modular plugins [].Epigenomics is an emerging area of research that generates a significant amount of specialized seque […]

library_books

Evolutionary plasticity of the NHL domain underlies distinct solutions to RNA recognition

2018
Nat Commun
PMCID: 5908797
PMID: 29674686
DOI: 10.1038/s41467-018-03920-7

[…] so very low pairing probabilities. The change to RNAplfold allowed us to efficiently fold not only short RNAs but also the full-length transcripts. For C. elegans, we used transcript annotations from WormBase (WS259) and extracted 5′-UTR, CDS, and 3′-UTR information from the file c_elegans.PRJNA13758.WS259.annotations.gff2.gz. […]

library_books

NCX DB: a unified resource for integrative analysis of the sodium calcium exchanger super family

2018
BMC Neurosci
PMCID: 5898058
PMID: 29649983
DOI: 10.1186/s12868-018-0423-2

[…] ned within NCX-DB was mined from UniProt (ver. June 2017) [] as well as the animal model organism databases that comprise the Alliance of Genome Resources (http://www.alliancegenome.org/). These are: WormBase (ver. WS260) [], XenBase (ver. 4.5.0) [], FlyBase (FB2017_04) [], the Zebrafish Information Network (ZFIN: https://zfin.org/), Mouse Genomics Informatics (http://www.informatics.jax.org/), an […]

Citations

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WormBase institution(s)
Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA; European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge, UK; Informatics and Bio-computing Platform, Ontario Institute for Cancer Research, Toronto, ON, Canada; Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK; Department of Genetics, Washington University School of Medicine, St Louis, MO, USA
WormBase funding source(s)
Supported by US National Human Genome Research Institute [U41-HG002223]; UK Medical Research Council [MR/L001220]; UK Biotechnology and Biological Sciences Research Council [BB/K020080].

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