How to search InParanoiDB9
Search by Protein
To search for a protein in InparanoiDB, select the "Search by Protein" tab on the home page. Here, you can search for a UnProt protein identifier, a gene name or a keyword. The keyword is used to search the protein description.If we find multiple entries in our database matching your search term, you will be presented a list from where you can select the protein you are interested in. This list can be filtered by species.
The resulting ortholog view will list all ortholog groups where your protein is present. This list can be filtered by one or multiple species to only show the ortholog groups including your protein in your selected species. The resulting list of ortholog groups can be downloaded as a csv-file or in OrthoXML format. Each ortholog group can be inspected in detail by clicking the "View group" button at the top of each ortholog group table.
The "View ortholog group" page will display a tree including all proteins present in the ortholog group. The tree is built using kalign (v.2.04) and Belvu (v4.44.1b). Next to each protein in the tree, the protein is drawn with its corresponding domains, obtained from pfam and analyzed with Domainoid. Domains labeled UNKx, are portions of the protein not assigned with a pfam domain, but analyzed in Domainoid as unknown domains. Domains having the same domain name are drawn in the same color, and UNK-domains are drawn in gray. The tree can be downloaded in newick format, as well as the sequences used to build the tree, and the aligned sequences produced by kalign by clicking the download buttons. When domain orthologs exists between any of the domains in the proteins included in the ortholog group, these will be displayed as tabs labeled "Domain orthogroup x". By clicking these tabs, a table will be shown, listing all domain orthologs in the domain-ortho-group, and their corresponding domains will be highlighted in the protein domain image. To see the detailed view of the domain ortholog group, click on the "View domain group" button.
Search by Species
To view all ortholog groups between two species, the "Search by species" tab on the home page can be used. To search for a species-pair, input the scientific name or taxID for two species and press search.The resulting page will show a list of all ortholog groups identified between your species. Each ortholog group can be inspected in detail by clicking the "View ortholog group" button at the top of each ortholog group table. By selecting the "View domain orthologs" switch, all domain orthologs detected between the two species will be listed. All pairwise protein -and domain orthologs can be donwloaded from the "downloads"-page.
Search by Domain
To search for a protein domain in InParanoiDB, go to the "Search by domain" tab on the home page. Enter the name or ID of a pfam domain and press search.The resulting view will display a list of all domains in the database having the corresponding name or ID. This list can be filtered by Species and/or protein name. Note that the same domain name can occur multiple times on the same protein, distinguished by the start and stop coordinate on the protein in question. Select the Protein domain you are interested in from the list.
The resulting ortholog view will list all ortholog groups where your domain is present. This list can be filtered by one or multiple species to only show the ortholog groups including your domain in your selected species. The resulting list of ortholog groups can be downloaded as a csv-file or in OrthoXML format. Each ortholog group can be inspected in detail by clicking the "View group" button at the top of each ortholog group table.
The "View Domain ortholog group" page will display a tree including all domains present in the ortholog group. The tree is built using kalign (v.2.04) and Belvu (v4.44.1b). Next to each domain in the tree, its corresponding protein is drawn with all of its domains, obtained from pfam and analyzed with Domainoid. The domain present in the ortholog group will be highlighted with a border and drawn wider than the other domains in the protein. Domains labeled UNKx, are portions of the protein not assigned with a pfam domain, but analyzed in Domainoid as unknown domains. Domains having the same domain name are drawn in the same color, and UNK-domains are drawn in gray. The tree can be downloaded in newick format, as well as the sequences used to build the tree, and the aligned sequences produced by kalign by clicking the download buttons. When protein orthologs exists between any of proteins that the domains in the ortholog group belongs to, these will be displayed as tabs labeled "Protein orthogroup x". By clicking these tabs, a table will be shown, listing all protein orthologs in the protein-ortho-group, and their corresponding protein names will be highlighted in the protein domain image. To see the detailed view of the protein ortholog group, click on the "View protein group" button. If any of the domains in the domain-group-proteins are members of other ortholog groups, an additional table will be shown, with one tab for each additional domain ortholog group. By clicking a tab, the domains in the group present in the protein drawing will be highlighted. o see the detailed view of an additional ortholog group, press tha "view domain group" button.