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Protocols

TriTrypDB specifications

Information


Unique identifier OMICS_03144
Name TriTrypDB
Restrictions to use None
Community driven No
Data access File download, Browse
User data submission Allowed
Version 34.0
Maintained Yes

Taxon


  • Invertebrates
    • Trypanosoma brucei

Subtools


  • TcruziDB
  • The strategies WDK

Documentation


Maintainer


  • person_outline Omar S. Harb

Additional information


http://tritrypdb.org/tritrypdb//showXmlDataContent.do?name=XmlQuestions.Tutorials

Publications for TriTrypDB

TriTrypDB citations

 (183)
call_split

Trypanosomal mitochondrial intermediate peptidase does not behave as a classical mitochondrial processing peptidase

2018
PLoS One
PMCID: 5919513
PMID: 29698456
DOI: 10.1371/journal.pone.0196474
call_split See protocol

[…] The gene encoding a putative MIP was identified using BLAST in the T. brucei genome database (www.tritrypdb.org). The T. brucei MIP sequence together with 32 selected MIP homologs, 7 genes of closely related thimet peptidases, 9 genes of OpdA and 6 genes of Dcp () obtained by a BLAST search were a […]

library_books

Cultured bloodstream Trypanosoma brucei adapt to life without mitochondrial translation release factor 1

2018
Sci Rep
PMCID: 5865105
PMID: 29572512
DOI: 10.1038/s41598-018-23472-6

[…] e loss of TbMrf1 and ensure some mt translation termination. In S. pombe, it has been demonstrated that the peptidyl-tRNA hydrolase Pth4 plays an overlapping role with Mrf1. A protein BLAST search on TriTrypDB revealed that TbPth4 (Tb927.6.2500), which contains a release factor domain, is the most obvious T. brucei ortholog of the yeast protein as they share 36% similarity and 21% identity (MUSCLE […]

library_books

UDP glycosyltransferase genes in trypanosomatid genomes have diversified independently to meet the distinct developmental needs of parasite adaptations

2018
BMC Evol Biol
PMCID: 5853035
PMID: 29540192
DOI: 10.1186/s12862-018-1149-6

[…] elative, C. fasciculata, UGTs as the query. Identified putative UGTs were named L. passim1–4 and C. acanthocephali1–4.UGT Sequences from Trypanosoma gambiense DAL972 and Trypanosoma evansi (hosted by TritrypDB v.28 (http://tritrypdb.org) []), and from Trypanosoma equiperdum (hosted by NCBI (http://www.ncbi.nlm.nih.gov/genome)) were also inspected. However, as they present the same repertoire as T. […]

library_books

Lipophosphoglycan 3 From Leishmania infantum chagasi Binds Heparin With Micromolar Affinity

2018
Bioinform Biol Insights
PMCID: 5858678
PMID: 29568220
DOI: 10.1177/1177932218763363

[…] ugust 28, 2015), parameterized with the values of E-threshold 0.0001, matrix blosum-62, filtering in low-complexity regions, gapped and hits 50. Genome analysis was performed in pBLAST implemented in TritrypDB. The signal peptide prediction was performed using SignalP 4.1 server,, and the presence of glycosylphosphatidylinositol (GPI)-anchor regions was assessed using GPI-SOM 1.5, big-PI Predictor […]

library_books

Building protein protein interaction networks for Leishmania species through protein structural information

2018
BMC Bioinformatics
PMCID: 5840830
PMID: 29510668
DOI: 10.1186/s12859-018-2105-6

[…] The sequences of the predict proteomes of L. braziliensis and L. infantum version 8.0 were obtained from the TriTrypDB database []. The use of computational methods to predict three-dimensional conformation of the proteins was necessary because just few structures for those proteomes were deposited in the Pr […]

library_books

SUMO polymeric chains are involved in nuclear foci formation and chromatin organization in Trypanosoma brucei procyclic forms

2018
PLoS One
PMCID: 5825156
PMID: 29474435
DOI: 10.1371/journal.pone.0193528

[…] d candidate proteins containing multiple SIMs that could be recruited by poly-SUMO chains. Briefly, we generated a FASTA-formatted version of the translated T. brucei coding sequences downloaded from TriTrypDB v9.0 [URL www.tritrypdb.org []] and used the ScanProsite server [URL http://www.expasy.org/tools/scanprosite []] to screen the entire proteome of species for the presence of the three classe […]

Citations

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TriTrypDB institution(s)
Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, UK; Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, GA, USA; Penn Center for Bioinformatics, University of Pennsylvania, Philadelphia, PA, USA; Department of Biochemistry, University of Cambridge, Cambridge, UK; Seattle Biomedical Research Institute, Seattle, WA, USA; Department of Global Health, University of Washington, Seattle, WA, USA; Center for Applied Genetic Technologies; Department of Genetics; Department of Computer Science, University of Georgia, Athens, GA, USA; Department of Medical Education and Biomedical Informatics, University of Washington, Seattle, WA, USA; Department of Biology, University of Pennsylvania, Philadelphia, PA, USA; Centre for Immunology and Infection, Department of Biology, University of York, Heslington, UK
TriTrypDB funding source(s)
Supported by Grant from the Bill & Melinda Gates Foundation to develop a TriTrypDB component of the EuPathDB project (Grant Number 50097.); Wellcome Trust (Grant Number WT085822MA.); Core funding from of the Wellcome Trust Sanger Institute by the Wellcome Trust (Grant Number WT085775/Z/08/Z). EuPathDB, which provides the infrastructure upon which TriTrypDB was constructed, is funded with federal funds from the National Institute of Allergy and Infectious Diseases, National Institutes of Health, Department of Health and Human Services, under Contract No. HHSN266200400037C.

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