Table 4.
Search comparisons PPTdb and several general purpose genomic databases
| Items | PPTdb | Entrez Gene | Uniprot | EuPathDB |
|---|---|---|---|---|
| Search term | nucleotide | nucleotide AND transporter AND Acanthamoeba castellanii str. Neff. | nucleotide transporter Acanthamoeba castellanii str. Neff. | nucleotide |
| a Pre-search settings | Click A. castellanii str. Neff | |||
| Set number of transmembrane domain: 1 | – | – | Click AmoebaDB | |
| One-click potential transporters: checked | 1135 genes for keyword search | |||
| Number of searched items | 12 GO terms | 76 genes with 1 transmembrane domain | ||
| 3 Prosite Patterns | No number of transmembrane domain filter | No number of transmembrane domain filter | ||
| 5 Pfams | c0 genes for annotation with “transporter” as keyword | |||
| Number of Genes after searching | 105 | b303 | b290 | c0/76 |
aThere are several search combinations of each database, it is reasonable that different search combinations may lead to different search results. This demo demonstrates one search strategy of each database
bNo transmembrane domain filter
cThere is no specific column for putative transporter genes of EuPathDB. Using “transporter” as keyword is the most possible search action used by most users