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Protocols

ToxoDB specifications

Information


Unique identifier OMICS_03168
Name ToxoDB
Restrictions to use None
Maintained Yes

Taxon


  • Invertebrates
    • Toxoplasma gondii

Maintainer


  • person_outline Jessica C. Kissinger

Publication for ToxoDB

ToxoDB citations

 (128)
library_books

MYR1 Dependent Effectors Are the Major Drivers of a Host Cell’s Early Response to Toxoplasma, Including Counteracting MYR1 Independent Effects

2018
MBio
PMCID: 5885026
PMID: 29615509
DOI: 10.1128/mBio.02401-17

[…] Raw reads were uploaded onto the CLC Genomics workbench 8.0 (Qiagen) platform for independent alignments against the human genomes (Ensembl.org/ hg19) and Toxoplasma type I GT1 strain (ToxoDB-24, GT1 genome). All parameters were left at their default values. The number of reads mapping to exons in the human and Toxoplasma genomes and the percentage of reads mapping to these genomes […]

library_books

TgTKL1 Is a Unique Plant Like Nuclear Kinase That Plays an Essential Role in Acute Toxoplasmosis

2018
MBio
PMCID: 5874906
PMID: 29559568
DOI: 10.1128/mBio.00301-18

[…] 2000 system.Data were analyzed using the Bioconductor suite of packages for the R computing environment (v. 3.3.2) and RStudio (v. 1.0.44). Reads were aligned to the Toxoplasma GT1 reference genome (ToxoDB v. 29; http://toxodb.org/toxo/) using the Rsubread package (v. 1.26.0) (), with default settings, followed by featureCounts () for gene-level count summarization. Following normalization and fi […]

library_books

Identification of a novel protein complex essential for effector translocation across the parasitophorous vacuole membrane of Toxoplasma gondii

2018
PLoS Pathog
PMCID: 5794187
PMID: 29357375
DOI: 10.1371/journal.ppat.1006828

[…] ype growth, even in vitro, and suggests that one or more effectors translocated by the MYR1/2/3-dependent machinery has a role in growth in HFFs.MYR2 is located on chromosome VIII and is predicted by ToxoDB (v32) to have two introns and encode a protein of ~32 kDa, including a predicted N-terminal signal peptide (probability 0.672 by SignalP 2.0 HMM) and, by TMpred, two transmembrane (TM) domains […]

library_books

The Expressed MicroRNA—mRNA Interactions of Toxoplasma gondii

2018
Front Microbiol
PMCID: 5759179
PMID: 29354114
DOI: 10.3389/fmicb.2017.02630

[…] ce characteristics of the samples, a large amount of reads were filtered and an older version of Tophat had to be used instead of current version v2.1.1. The annotation file for the T. gondii genome (ToxoDB-25_TgondiiME49) was downloaded from toxodb.org along with its genome. An in-house script was used to count mapped reads (https://github.com/erkinacar5/SortedNucleotideCounter). Genes with less […]

call_split

Metallopeptidases of Toxoplasma gondii: in silico identification and gene expression

2018
PMCID: 5939537
PMID: 29737275
DOI: 10.1051/parasite/2018025
call_split See protocol

[…] according to their MEROPS classification in families, beyond their amino-, carboxy- or endopeptidase predicted activity. Putative metallopeptidase Toxoplasma genes were identified from the T. gondii ToxoDB database, (http://toxodb.org/toxo/, Release 29) using peptidase family domain (PFAM motifs) recorded in the MEROPS Database (https://www.ebi.ac.uk/merops/) for this family of enzymes. The TGME4 […]

library_books

A conserved ankyrin repeat containing protein regulates conoid stability, motility and cell invasion in Toxoplasma gondii

2017
Nat Commun
PMCID: 5740107
PMID: 29269729
DOI: 10.1038/s41467-017-02341-2

[…] ogeny was inferred with PhyML and aLRT, and the tree generated using TryDyn. Protein domains were analyzed with InterPro (https://www.ebi.ac.uk/interpro/). Classification of GO terms was performed in TOXODB (http://toxoDB.org). […]

Citations

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ToxoDB institution(s)
Department of Biology, Department of Genetics, Center for Bioinformatics, University of Pennsylvania, Philadelphia, PA, USA

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