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Protocols

GiardiaDB specifications

Information


Unique identifier OMICS_03161
Name GiardiaDB
Restrictions to use None
Community driven No
Data access Browse
User data submission Allowed
Maintained Yes

Taxon


  • Invertebrates
    • Giardia intestinalis
    • Trichomonas vaginalis

Maintainer


  • person_outline Omar S. Harb

Publication for GiardiaDB

GiardiaDB citations

 (37)
call_split

Secreted Giardia intestinalis cysteine proteases disrupt intestinal epithelial cell junctional complexes and degrade chemokines

2018
PMCID: 5955458
PMID: 29726306
DOI: 10.1080/21505594.2018.1451284
call_split See protocol

[…] atabase searches were performed using the Sequest algorithm, embedded in Proteome Discoverer 1.4 (Thermo Fisher Scientific), towards a FASTA database containing proteins from Giardia, downloaded from giardiadb.org/common/downloads/release5.0/GintestinalisAssemblageA/. The search criteria for protein identification were set to at least one matching peptide of 95% confidence level per protein. In ad […]

call_split

Beaver Fever: Whole Genome Characterization of Waterborne Outbreak and Sporadic Isolates To Study the Zoonotic Transmission of Giardiasis

2018
PMCID: 5917422
PMID: 29695621
DOI: 10.1128/mSphere.00090-18
call_split See protocol

[…] e a coverage of >4. We assessed the assemblage type of each isolate by mapping reads from each isolate to the reference genomes of G. duodenalis (assemblages A, B, and E) that were retrieved from the GiardiaDB (http://giardiadb.org) (). To remove any potential contaminant contigs (non-Giardia reads), contigs were mapped to the NCBI nt database using BLASTn megablast (-best_hit_overhang 0.25 -best_ […]

library_books

The draft genome of Kipferlia bialata reveals reductive genome evolution in fornicate parasites

2018
PLoS One
PMCID: 5874029
PMID: 29590215
DOI: 10.1371/journal.pone.0194487

[…] For the surface membrane protein survey, 253 variant-surface proteins in Giardia intestinalis and 415 cysteine-rich proteins in Spironucleus were obtained from GiardiaDB (http://giardiadb.org/giardiadb/) and used in blastp or tblastn searches against the K. bialata predicted protein dataset or the genome including the small scaffolds discarded in the gene pr […]

library_books

Differential protein expression and post translational modifications in metronidazole resistant Giardia duodenalis

2018
GigaScience
PMCID: 5913674
PMID: 29688452
DOI: 10.1093/gigascience/giy024

[…] Interpro protein domains, and structure annotations where available. Gene set enrichment analysis (GSEA) was performed on differentially expressed proteins using the DAVID bioinformatics resource []. GiardiaDB.org open reading frame identifiers from combined up- and downregulated proteins in each MtzR isolate were converted to gene identifiers using the National Center for Biotechnology Informatio […]

call_split

Giardia secretome highlights secreted tenascins as a key component of pathogenesis

2018
GigaScience
PMCID: 5887430
PMID: 29385462
DOI: 10.1093/gigascience/giy003
call_split See protocol

[…] To look for sequence similarities between proteins of interest from the same protein family, the coding sequences of these proteins were retrieved from GiardiaDB (v 3.1, 4.0, and 5.0), aligned, and compared using ClustalW.Phylogenetic trees were built for these proteins via the maximum likelihood approach using MEGA software (v. 6.06). […]

call_split

Characterization of the Giardia intestinalis secretome during interaction with human intestinal epithelial cells: The impact on host cells

2017
PLoS Negl Trop Dis
PMCID: 5739509
PMID: 29228011
DOI: 10.1371/journal.pntd.0006120
call_split See protocol

[…] ultures were identified by performing separate searches against the fasta files of the Giardia proteome for each isolate (GS clone containing 4470 entries and WB clone 9667 entries) (available at www.giardiadb.org; giardiadb.org/common/downloads/release5.0/). The fasta file for human proteins was downloaded from Uniprot 2015–05 and contained 20192 entries. Proteins in co-cultures were searched aga […]

Citations

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GiardiaDB institution(s)
Center for Tropical & Emerging Global Diseases, University of Georgia, Athens, GA, USA; Penn Center for Bioinformatics, University of Pennsylvania, Philadelphia, PA, USA; Department of Medical Parasitology, New York University Langone Medical Center, New York, NY, USA; Center for Applied Genetic Technologies, University of Georgia, Athens, GA, USA; School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Department of Genetics, University of Georgia, Athens, GA, USA; Department of Computer Science, University of Georgia, Athens, GA, USA; Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, MA, USA; Department of Biology, University of Pennsylvania, Philadelphia, PA, USA
GiardiaDB funding source(s)
This tool was supported by the National Institute of Allergy and Infectious Diseases, the Department of Health and Human Services and the National Institutes of Health (HHSN266200400037C).

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