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AmoebaDB specifications

Information


Unique identifier OMICS_03152
Name AmoebaDB
Restrictions to use None
Maintained Yes
Wikipedia https://en.wikipedia.org/wiki/AmoebaDB

Maintainer


  • person_outline Omar S. Harb

Publication for AmoebaDB

AmoebaDB citations

 (17)
library_books

Hetero oligomer of dynamin related proteins participates in the fission of highly divergent mitochondria from Entamoeba histolytica

2017
Sci Rep
PMCID: 5647421
PMID: 29044162
DOI: 10.1038/s41598-017-13721-5

[…] To survey Entamoeba candidate proteins involved in the fission and fusion of mitosomes in AmoebaDB, we performed BLASTP search using sequences of full-length proteins known to be involved in mitochondrial fission in human, yeast, and Dictyostelium, as query. Survey was also conducted using […]

library_books

Membrane Trafficking Modulation during Entamoeba Encystation

2017
Sci Rep
PMCID: 5634486
PMID: 28993644
DOI: 10.1038/s41598-017-12875-6

[…] 46 - MF361261.The assembled transcripts were preliminary annotated against the E. invadens IP-1 (JCVI) and E. histolytica HM-1:IMSS (JCVI) annotated transcripts and proteomes (publically available at amoebaDB.org). All-against-all nucleotide BLASTN and BLASTX (translating a nucleotide query in six reading frames) searches were conducted. Annotations were assigned to the RNA-Seq transcripts when hi […]

library_books

Proteome analysis of excretory secretory proteins of Entamoeba histolytica HM1:IMSS via LC–ESI–MS/MS and LC–MALDI–TOF/TOF

2016
PMCID: 5120466
PMID: 27895543
DOI: 10.1186/s12014-016-9135-8

[…] les were eluted using a gradient of B from 5 to 100% in 100 min. The fragmentation technique used was collision induced dissociation (CID). De Novo sequencing and database matching against a combined AmoebaDB_4.1 and cRAP (‘protein contaminants database’) was performed using Peaks Studio Version 7 (Bioinformatics Solution, USA). The cRAP includes the possible contaminant proteins in this study suc […]

call_split

Overexpression of Differentially Expressed Genes Identified in Non pathogenic and Pathogenic Entamoeba histolytica Clones Allow Identification of New Pathogenicity Factors Involved in Amoebic Liver Abscess Formation

2016
PLoS Pathog
PMCID: 5004846
PMID: 27575775
DOI: 10.1371/journal.ppat.1005853
call_split See protocol

[…] Libraries were denatured and diluted to final concentration of 8 pM for sequencing on the MiSeq platform following the manufacturer’s instructions. Reads were aligned to E. histolytica transcriptome (AmoebaDB 28, released 30 March 2016) using Bowtie 2 version 2.2.3 [] and differential expression was analysed using DESeq [] version 1.18. […]

call_split

Evaluation of the mechanisms of intron loss and gain in the social amoebae Dictyostelium

2015
BMC Evol Biol
PMCID: 4683709
PMID: 26678305
DOI: 10.1186/s12862-015-0567-y
call_split See protocol

[…] um, Dictyostelium purpureum, P. pallidum, and Dictyostelium fasciculatum were downloaded from DictyBase [, ] in March 2014, and those of E. histolytica (HM1IMSS, version 3.1) were downloaded from the AmoebaDB [, ]. We discarded genes with obvious annotation errors, such as those that did not contain coding sequences that were composed of multiples of three nucleotides or those that appeared to con […]

library_books

In Entamoeba histolytica, a BspA family protein is required for chemotaxis toward tumour necrosis factor

2015
PMCID: 5349171
PMID: 28357299
DOI: 10.15698/mic2015.07.214

[…] zed trophozoites, suggesting that an E. histolytica surface protein shared a common epitope with the hTNFR1.The amino acid sequence of hTNFR1 was used in a BLAST search of the amoebic proteome in the AmoebaDB. Of 8201 ORFs representing the amoebic proteome, a single sequence was identified (E-value: 3.5x10-7; entry EHI_016490; predicted molecular mass: 140 kDa) as comprising a TNFR domain (Figure […]

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AmoebaDB institution(s)
Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, GA, USA

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