JIPS was conceived as a tool to help biologists manage and analyze the results generated by large numbers of InterProScan searches. It takes considerable hands-on time for a researcher to evaluate the results of even one InterProScan search when more than a few signatures are hit, and this problem is compounded when multiple proteins are searched. Reviewing results of repeated scans performed with different versions of InterPro is similarly tedious and time-consuming. Therefore, a primary goal in creating JIPS was to provide users with a tracking tool to quickly summarize differences between repeated searches. A second objective was to assist researchers in analyzing these results through comparative genomics.
JIPS is particularly useful for performing a series of InterProScan searches with a group of diverse protein orthologs. Investigating an InterPro signature that only appears in one, or a few, of the orthologs can be very productive. In some cases, comparison of the sequence containing the motif to the other orthologs may lead to the researcher detecting a variation of the signature pattern in these sequences. This would suggest that the original hit is significant and that the signature pattern may need to be generalized to reflect this new set of proteins. On the other hand, the researcher may conclude that the signature is indeed only present in the single sequence, suggesting that it is spurious (i.e. a random match). In both situations, running InterProScan on only a single member of the group would yield different, and possibly misleading, results.
Browsing JIPS Hits
After starting JIPS, a general user can begin browsing a given JIPS database by either double-clicking on the database node in the left-hand panel of the JIPS Management Console, or selecting the Browse virus/organism item from the Action menu (Figure 2). The JIPS Browse Organism/Virus window then opens (Figure 3), providing the user with a list of all the viruses/organisms in this particular JIPS database. As an example, we chose the VBRC poxvirus database, containing 10,566 protein sequences from 54 complete poxvirus genomes. These were searched against the InterPro database with InterProScan, generating 27,182 signature hits. The next step is to select a virus/organism of interest and set display preferences for the InterProScan results. The user chooses 1) a cutoff date, used by JIPS to determine whether a given hit should be marked as new, and 2) the sorting mode (used to sort the list of genes that appears in the next window).
Double-clicking on the virus/organism of interest, or clicking on the View Summary of Hits button, will open the Summary of InterPro Hits window for that virus/organism. Figure 4 shows a sample summary of hits for Variola major virus strain Bangladesh-1975. Each row in the window represents a protein encoded by this viral genome; from left to right, it lists the protein name, the total number of non-redundant hits, and the number of new hits (i.e. hits found since the cutoff date). A row is colored red if at least one of its hits was recorded after the cutoff date; otherwise, it is colored white. We selected the VARV-Bsh-B1R gene, which had a total of 5 signature hits, and clicked the Show InterPro Hits button. The JIPS Hits Manager window (Figure 5) opens, showing 5 individual signatures (pink) belonging to a total of 3 InterPro categories (red). If a given row in the table (corresponding to an InterPro category or individual hit) is selected, its hit score(s) and match region(s) are displayed, together with the query protein sequence, in the lower half of the window. Clicking on the Location button will highlight the region on the query sequence matching the signature hit. Finally, double-clicking on a row (or clicking the "Open Web Link" button) will open a web browser containing the signature home page; e.g. a Pfam signature from the Pfam database.
Comparing/Aligning Orthologs
At the bottom of the JIPS Hits Manager window are a series of buttons enabling the user to perform further analysis. Clicking on the Compare with Orthologs button opens a menu from which the user selects the database proteins to use in the comparison. A color-coded matrix-style graphic (Orthologs Comparison window) is then automatically generated, clearly showing which signatures are also present in the selected orthologs (Figure 6). In this example, we compared the InterProScan results for VARV-Bsh-B1R with those for orthologous proteins in the JIPS database. From the results in Figure 6, it is apparent that the PROSITE signature PS00108 (ser/thr protein kinase active site) is present in VARV-Bsh-B1R but absent from a number of the orthologs. Signatures present in an ortholog but missing from the original sequence can be easily found by clicking the button representing the protein of interest in the Orthologs Comparison window; a JIPS Hits Manager window for the ortholog will open.
Further analysis can be performed by clicking the Align Orthologs in BBB button (in the JIPS Hits Manager window); this will bring up a list of all available orthologs. JIPS will automatically retrieve the selected protein sequences from the database, submit them to MUSCLE [19] for alignment, and open the results in the MSA editor, BBB [14, 16]. The signatures are shown as comments beneath the alignment and a consensus sequence can be displayed (Figure 7). From these results it is apparent that the reason that the PS00108 signature (regular expression: [LIVMFYC]-x- [HY]-x-D- [LIVMFY]-K-x(2)-N- [LIVMFYCT](3)) does not appear in some of the orthologs is due to a single amino acid substitution; they contain alanine as the penultimate residue of the motif.
Saving Results
Although the JIPS database is itself a repository of InterPro search results, JIPS also provides a function (Save as BBB File button) that adds the signatures as comments (annotations) to a protein sequence and writes a file in BBB format. This allows simple reviewing and sharing of final results. The files are saved on the user's local computer and can be independently loaded into BBB. If required, the user can edit/add/delete these comments from within BBB and the other comment-associated features of this program are also available to the user.
The signatures can also be written to a BBB file as part of the MSA generated by the Align Orthologs in BBB feature (Figure 7). In this case, to conserve space in the viewer, the comments are only written for the primary protein