InterProScan search

Data access component contains a module for running InterProScan remotely against a European Bioinformatics Institute (EBI) database. Similar to other components (for example, BLAST), the query is selected interactively by clicking structure or sequence name button. Alternatively, a file containing a sequence or structure may be specified. The advantage of interactive query selection is that each domain hit can be mapped to the loaded structure or sequence.

Settings that can be changed by the user include specific searches to be run at the server, as well as selection of protein vs. DNA and choice of check of the precomputed results stored at the EBI server first.

The search normally takes under one minute, but the exact time depends on the size of the sequence and parameters, such as cutoff value and maximum number of hits. Once the search is completed, the list of hits is displayed. The view shows name, accession number, description and e-value for each hit. The user may select a single result of multiple hits and load them into the sequence viewer. In addition, it is possible to view the local alignment of each hit produced by BLAST. Finally, the raw BLAST output file may be saved locally.

The display options include mapping of the selected domain hit to the display - the corresponding region of the structure and/or sequence is selected. In addition, a browser window with detailed information from the source database can be open. In addition, results of the search can be saved in XML format for further parsing.