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Fig. 2 | BMC Bioinformatics

Fig. 2

From: Pathogenic Protist Transmembranome database (PPTdb): a web-based platform for searching and analysis of protist transmembrane proteins

Fig. 2

The interactive web interface (a) In step 1, users can choose interested species by clicking the species name of the species selector panel. The full genus, species and strain name is pop-up while the cursor hover on the species name. b Step 2 provides four kinds of filters. The filter 2–1 delivers the sequence identity results as a Venn diagram; the left (yellow circle) represents genes dissimilar to human proteins, while the intersecting region (color mixed of yellow and red) shows the human homolog transporter genes. Users can select either left, right, or both to narrow down the search gene sets. The filter 2–2 is the transmembrane-domain (TM) filter for the number of transmembrane domains allows users to select genes with a specific number of TMs. The iterative functional mining panel (filter 2–3), allowing the user to execute multiple-layer selection with multiple independent queries, shown in (c). All the selected functional description keywords of protein families including GO terms, Prosite patterns and profiles, Pfams, and TIGRFAMs are combined into a functional filter. The Advanced options contains the BLASPp parameter settings and known transporter GO filter. d The annotation table is implemented by type-n-search data table technology which allows the user to type any keyword characters, with or without complete spelling, to narrow down the search size. All the secondary search results can be passed into the middle panel, and the functional search can be performed iteratively. Users can be re-directed to the external databases by clicking the hyperlink on any underlined entries, such as GO IDs and gene IDs. Additionally, there is a check box on the first column of every entry in table which allows users to selected genes and apply to step 2 for further functional selection. e Genes filtered by four filters (TM filter, one-click transporter GO filter, sequences homologous filter, and iterative functional filter) are displayed by summary charts which list the top 10 dominant functional elements, including GO, PROSITE pattern, PROSITE profile, Pfam, and superfamily. The annotations, protein sequences, and BLASTp alignment results of selected genes are compressed into a single file and can be downloaded through the download link on the top side menu of the annotation Table. f Compare2 is designed for two protists systematically compared based on functional annotations. The Venn diagrams deliver the common or unique functional elements clearly, and all relative genes can be listed in the data table below

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