WormBase Converter protocols

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WormBase Converter specifications

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Unique identifier OMICS_14402
Name WormBase Converter
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Input data The WormBase Gene ID used by the WormBase database, the name given to a gene with a specific format, the name given to a CDS (coding sequence), the name given to a transcript, the name given to a gene.
Output data A conversion of the gene IDs is performed to give the output ID wanted.
Operating system Unix/Linux, Mac OS, Windows
Computer skills Medium
Stability Stable
Source code URL http://wormbasemanager.sourceforge.net/downloads/WBConverter__Local__Sources.tar.gz
Maintained Yes

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  • person_outline Jonathan Ewbank <>

Publication for WormBase Converter

WormBase Converter in pipelines

 (2)
2016
PMCID: 5411242
PMID: 27600703
DOI: 10.1080/21505594.2016.1222334

[…] performed as previously described. to compare qpcr and microarray data, a one sample, 2-tailed t-test was performed., all gene lists, including those culled from the literature, were passed through wormbase converter using the ws220 genome release as the output (references are noted in table s7). a total of 20,834 ws220 genes are represented by 1 or more probes in the agilent c. elegans v2 […]

2014
PMCID: 4207467
PMID: 25340560
DOI: 10.1371/journal.pgen.1004609

[…] points, 2 biological replicates were assessed. the microarray data was deposited in the gene expression omnibus database: gse54212., gene lists were culled from the literature and passed through wormbase converter using the ws220 genome release as the output (references are noted in ). a total of 20,834 ws220 genes are represented by 1 or more probes in the agilent c. elegans v2 array […]

WormBase Converter in publications

 (5)
PMCID: 5684781
PMID: 29152379
DOI: 10.1038/cddiscovery.2017.73

[…] based on previous studies, and genes were classified as intestine and neuron associated. in order to compare between different releases of the wormbase, we used the software ‘wormbase converter’., the differentially expressed genes identified in time-lapse analyses were used to construct the weighted gene co-expression network using the r package wgcna (version 1.51)., […]

PMCID: 5386862
PMID: 28179390
DOI: 10.1534/g3.117.039057

[…] created using a cutoff p value of <0.05, twofold change (table s3 in file s2). for subsequent analyses, the list of upregulated genes was curated by removing duplicates and passed through the wormbase converter () using the ws220 genome release as the output. for gene enrichment analysis, gene lists were selected from the literature and passed through the wormbase converter () using […]

PMCID: 4145682
PMID: 25118236
DOI: 10.1128/mBio.01235-14

[…] a cutoff p value of <0.05, 2-fold change (see in the supplemental material). for subsequent analyses, the list of up- and downregulated genes was curated by removing duplicates and using the wormbase converter (http://wormbasemanager.sourceforge.net), wb220., whole-worm lysates were prepared in the presence of protease and phosphorylase inhibitors. active pmk-1 was detected using […]

PMCID: 3961378
PMID: 24651852
DOI: 10.1371/journal.pone.0092552

[…] gene ontology browser that exports data to revigo, another web based tool that summarizes ontology data and plots them onto 2d space based on semantic similarity measures , ., for ease analysis, the wormbase converter tool (http://www.ciml.univ-mrs.fr/applications/wb_converter/) was used to convert the gene names from the wbcel235 release to ws230 release gene names . ease was then performed […]

PMCID: 3275553
PMID: 22347378
DOI: 10.1371/journal.pone.0030482

[…] (). because of the structure of the underlying database, moslocator requires sequence or transcript names as an input. these identifiers can be found in wormbase, or by using the online resource wormbase converter that allows any of the common c. elegans identifiers to be converted to the gene sequence identifier (). alleles associated with any number of genes can be found with moslocator […]

WormBase Converter institution(s)
Centre d’Immunologie de Marseille-Luminy, Université de la Méditerranée, Marseille, France; INSERM, U631, Marseille, France; CNRS, UMR6102, Marseille, France; Institut de Mathématiques de Luminy, Marseille, France; Department of Genetics, Yale University School of Medicine, New Haven, CT, USA; Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
WormBase Converter funding source(s)
This research was funded by institutional grants from the CNRS and INSERM, by the ANR FUNGENOMICS grant, by the European Community’s FP7/2007-2013 (grant agreement nu PIEF-GA-2008-220008), by the modENCODE Project at the National Human Genome Research Institute in the National Institutes of Health (USA).

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