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TrichDB specifications

Information


Unique identifier OMICS_03162
Name TrichDB
Restrictions to use None
Community driven No
Data access Browse
User data submission Not allowed
Maintained Yes

Taxon


  • Invertebrates
    • Trichomonas vaginalis

Documentation


Maintainer


  • person_outline Omar S. Harb

Publication for TrichDB

TrichDB citations

 (17)
library_books

Metabolomic profiling and stable isotope labelling of Trichomonas vaginalis and Tritrichomonas foetus reveal major differences in amino acid metabolism including the production of 2 hydroxyisocaproic acid, cystathionine and S methylcysteine

2017
PLoS One
PMCID: 5739422
PMID: 29267346
DOI: 10.1371/journal.pone.0189072

[…] Putative genes for selected metabolic enzymes were identified by tblastn search of the whole genome shotgun contigs (wgs) database, BioProject ID 345179. Model protein sequences were obtained from TrichDB (trichdb.org) for T. vaginalis or KEGG (www.genome.jp/kegg) for other organisms. […]

library_books

Genetic Indicators of Drug Resistance in the Highly Repetitive Genome of Trichomonas vaginalis

2017
Genome Biol Evol
PMCID: 5522705
PMID: 28633446
DOI: 10.1093/gbe/evx110

[…] P effects from the final data set were predicted using SnpEff (), and functional categories were determined using the Kyoto Encyclopedia of Genes and Genomes (KEGG) (; ) metabolic enrichment tools in TrichDB (). […]

library_books

Epigenome mapping highlights chromatin mediated gene regulation in the protozoan parasite Trichomonas vaginalis

2017
Sci Rep
PMCID: 5366954
PMID: 28345651
DOI: 10.1038/srep45365

[…] red using an NGS QC Toolkit v2.3 to remove reads with low-quality bases (quality score >20). Genomic scaffolds of T. vaginalis, sequences of annotated genes, and genomic features were downloaded from TrichDB v2.0 (http://trichdb.org/trichdb/); repeated genes were discarded. High-quality reads were mapped to the T. vaginalis genome using RSEM with Bowtie2 v2.0.0-beta7. The expression level of each […]

library_books

Optimal Reference Genes for Gene Expression Normalization in Trichomonas vaginalis

2015
PLoS One
PMCID: 4579074
PMID: 26393928
DOI: 10.1371/journal.pone.0138331

[…] genase (GAPDH), elongation factor (Efa), and DNA topoisomerase II (DNATopII) (). The nucleotide sequences of all candidate reference genes were obtained from the T. vaginalis genome project database (TrichDB http://trichdb.org/trichdb/), where more than one sequence was found. To select only one nucleotide sequence for each gene, the following approach was used: all sequences obtained with a score […]

call_split

Conservation of Transit Peptide Independent Protein Import into the Mitochondrial and Hydrogenosomal Matrix

2015
Genome Biol Evol
PMCID: 4607531
PMID: 26338186
DOI: 10.1093/gbe/evv175
call_split See protocol

[…] ected to a Mascot server (version 2.4.1, Matrix Sciences, London, UK) with default parameters for spectrum selection. Searches were carried out using 59,672 protein entries and protein sequences from TrichDB (release 1.3 from 26.5.2011) applying the following parameters: Mass tolerance precursor (analyzed in the Orbitrap part of the instrument) 10 ppm, mass tolerance fragment spectra (analyzed in […]

call_split

Genome Wide Analyses and Functional Classification of Proline Repeat Rich Proteins: Potential Role of eIF5A in Eukaryotic Evolution

2014
PLoS One
PMCID: 4218817
PMID: 25364902
DOI: 10.1371/journal.pone.0111800
call_split See protocol

[…] nd Saccharomyces Genome Database (SGD, http://www.yeastgenome.org/download-data/sequence) for the retrieval of verified ORFs encoded protein sequence for E. coli and S. cerevisiae, respectively. The TrichDB (http://trichdb.org/common/downloads/Current_Release/) , PomBase (ftp://ftp.ensemblgenomes.org/pub/fungi/current/fasta/schizosaccharomyces_pombe/pep/) and TAIR (ftp://ftp.arabidopsis.org/home […]

Citations

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TrichDB 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

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