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GeneDB specifications

Information


Unique identifier OMICS_03160
Name GeneDB
Restrictions to use None
Maintained No
Wikipedia https://en.wikipedia.org/wiki/GeneDB

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Publication for GeneDB

GeneDB citations

 (209)
library_books

Analysis of the Antigenic and Prophylactic Properties of the Leishmania Translation Initiation Factors eIF2 and eIF2B in Natural and Experimental Leishmaniasis

2018
PMCID: 5895769
PMID: 29675401
DOI: 10.3389/fcimb.2018.00112

[…] The genes encoding L. infantum eIF2 (LieIF2) and eIF2B (LieIF2B) factors were identified in the sequence database of L. infantum (www.genedb.org) by BLAST searches employing the S. cerevisiae orthologs sequences. We retrieved the entries annotated as the putative α, β, and γ subunits of the LieIF2 and α, β, and δ subunits of the Lie […]

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

[…] 45, L. braziliensis MHOM/BR/75/M2904, Leptomonas pyrrhocoris H10, and Crithidia fasciculata Cf-Cl hosted by TritrypDB v.28 (http://tritrypdb.org) []; Bodo saltans hosted by the GeneDB website (http://genedb.org) []; and Angomonas deanei and Strigomonas culicis hosted by Ensembl Protists v.31 (http://protists.ensembl.org). Additionally, a sequence similarity search with tBLASTn using T. brucei, L. […]

library_books

Landscape of the spliced leader trans splicing mechanism in Schistosoma mansoni

2018
Sci Rep
PMCID: 5832876
PMID: 29497070
DOI: 10.1038/s41598-018-22093-3

[…] . To identify the SLTS targets, RNA-Seq Filtered reads trimmed by the SL sequence and SL Trapping reads were aligned to the genomic sequence of S. mansoni (5th version), which was downloaded from the GeneDB, using the TopHat2 mapper version 2.0.9 (with -i 10 -I 30000 -p 8 -library-type fr-unstranded parameters). Subsequently, all SRA RNA-Seq reads from the cercariae stage were aligned to the genom […]

library_books

Genome‐wide mosaicism in divergence between zoonotic malaria parasite subpopulations with separate sympatric transmission cycles

2018
Mol Ecol
PMCID: 5918592
PMID: 29292549
DOI: 10.1111/mec.14477

[…] ameters (LEADING:3 TRAILING:3, SLIDINGWINDOW:4:10 MINLEN:36).Trimmed FASTQ reads for individual isolates were then aligned against the version 2.0 of P. knowlesi strain H reference genome (http://www.genedb.org/Homepage/Pknowlesi, genome annotation March 2014, accessed December 2015) using the burrows‐wheeler aligner software version 0.7 with the BWA‐MEM algorithm and default parameters (Li, ). Th […]

library_books

Microexon gene transcriptional profiles and evolution provide insights into blood processing by the Schistosoma japonicum esophagus

2018
PLoS Negl Trop Dis
PMCID: 5825161
PMID: 29432451
DOI: 10.1371/journal.pntd.0006235

[…] ng MEG-8.2 and -8.3, where the lack of a T. regenti equivalent to the latter gene and ambiguous tree topology () makes the timing of gene duplication uncertain. Searching of S. mansoni proteins v4 on GeneDB, using HMMER with an HMM based on an alignment of the conserved C-terminal domain of MEG-8 family members, also returns a hitherto unsuspected but significant match (e-value 0.0088) with SmMEG- […]

call_split

Dipeptidyl peptidase 3, a novel protease from Leishmania braziliensis

2018
PLoS One
PMCID: 5755878
PMID: 29304092
DOI: 10.1371/journal.pone.0190618
call_split See protocol

[…] The sequences of DPP3 from human (UniProt ID: Q9NY33-1) and L. braziliensis (LbrM.05.0940) were retrieved from the UniProt (http://www.uniprot.org/uniprot/Q9NY33) database and GeneDB server (http://www.genedb.org/Homepage), respectively. The sequences were submitted to a multiple sequence alignment at the Clustal Omega server (http://www.ebi.ac.uk/Tools/services/web_clustal […]

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GeneDB institution(s)
Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, UK

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