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Protocols

WormBase ParaSite specifications

Information


Unique identifier OMICS_19196
Name WormBase ParaSite
Restrictions to use None
Community driven No
Data access Browse
User data submission Not allowed
Version WBPS9
Maintained Yes

Maintainer


  • person_outline Kevin L. Howe

Publication for WormBase ParaSite

WormBase ParaSite citations

 (28)
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 an […]

library_books

TGF β mimic proteins form an extended gene family in the murine parasite Heligmosomoides polygyrus

2018
PMCID: 5904571
PMID: 29510118
DOI: 10.1016/j.ijpara.2017.12.004

[…] ger Institute, UK (BioProject PRJEB1203, (International Helminth Genomes Consortium, 2018)) and the Blaxter Laboratory at the University of Edinburgh, UK (BioProject PRJEB15396), both accessible from WormBase ParaSite, https://parasite.wormbase.org (, ).Phylogenetic analysis was performed using MEGA7 () and an inferred evolutionary tree drawn using the Neighbour-Joining method (). […]

library_books

Evolutionary fates of universal stress protein paralogs in Platyhelminthes

2018
BMC Evol Biol
PMCID: 5793430
PMID: 29390964
DOI: 10.1186/s12862-018-1129-x

[…] verrini, Clonorchis sinensis, Echinococcus granulosus, Echinococcus multilocularis, Echinococcus canadensis, Taenia solium, Hymenolepis microstoma, and Schmidtea mediterranea) were extracted from the WormBase ParaSite and SmedGD databases [, ] using the USP Pfam code PF00582 and the keyword “universal stress protein”. Orthologs relationship were initially obtained by reciprocal BLASTn, and confirm […]

library_books

Pleiotropic alterations in gene expression in Latin American Fasciola hepatica isolates with different susceptibility to drugs

2018
PMCID: 5781333
PMID: 29368659
DOI: 10.1186/s13071-017-2553-2

[…] at the CPqRR sequencing facilities at FIOCRUZ, Belo Horizonte, to obtain 117 million 76 bp pair end reads. The resulting sequences were quality trimmed and mapped to the F. hepatica reference genome (WormBase Parasite Acc: PRJEB6687) [] using CLC Genomics Workbench v7 (Qiagen, Aarhus C, Denmark) with default parameters. A good coverage of predicted genes (over 80%) was observed. A summary of the n […]

call_split

Flatworm specific transcriptional regulators promote the specification of tegumental progenitors in Schistosoma mansoni

2018
eLife
PMCID: 5927768
PMID: 29557781
DOI: 10.7554/eLife.33221.033
call_split See protocol

[…] otal number of reads per gene was determined by mapping the reads to the S. mansoni genome using STAR (version 020201) (). S. mansoni genome sequence and GTF files used for mapping were acquired from Wormbase Parasite (). Pairwise comparisons of differential gene expression were performed with DESeq2 (version 1.12.2) (). To determine which genes showed the highest level of enrichment in the variou […]

call_split

The RIO protein kinase encoding gene Sj riok 2 is involved in key reproductive processes in Schistosoma japonicum

2017
PMCID: 5727939
PMID: 29233188
DOI: 10.1186/s13071-017-2524-7
call_split See protocol

[…] 62.1) was obtained by using the BlastN algorithm (https://blast.ncbi.nlm.nih.gov/Blast.cgi). The cDNA sequence that mapped to the gene in the draft genome was obtained from the S. japonicum genome of WormBase ParaSite (http://parasite.wormbase.org/ftp.html). Exon-intron boundaries in genomic sequences were determined by blast analyses using cDNA sequences as probes. The Sj-RIOK-2 protein sequence […]

Citations

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WormBase ParaSite institution(s)
European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK; Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
WormBase ParaSite funding source(s)
Supported by the UK Biotechnology and Biological Sciences Research Council [BB/K020080].

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