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AmoebaDB specifications


Unique identifier OMICS_03152
Name AmoebaDB
Restrictions to use None
Maintained Yes


  • person_outline Omar S. Harb

Publication for AmoebaDB

AmoebaDB citations


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

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 […]


Membrane Trafficking Modulation during Entamoeba Encystation

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 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 […]


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

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 […]


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

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. […]


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

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 […]


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

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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