From Human Salivary Proteome Wiki
InterProScan
InterProScan is a sequence analysis program that is used to identify sequence features within a protein. The tool uses a collection of known signatures from the InterPro database to scan the entire protein sequence for similar patterns. The search routines used include: BlastProDom (Blastall), FingerPrintScan, Hmmpfam, ScanRegExp + ProfileScan, SignalPHMM and TMHMM2.0 (see reference #1 for details). Once found, if a region is above a certain "minimum score" established by human experts, the program determines that the given identified signature does exist in the protein. Refer to this tutorial for more details about InterProScan.
See also: Help:Protein Signatures
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Using InterProScan
There are two ways to launch InterProScan in this wiki as described below. Both methods will submit the input sequences to the European Bioinformatics Institute (EBI) for analyses through Web services.
InterProScan special page
The interface on Special:InterProScan lets you submit your own amino acid sequences. To start a job, simply enter or paste the sequence in the text box, and press Search.
Link from protein pages
A large number of proteins have been scanned by the program at some point. The results are stored as sequence annotations, each indicating the signature found, and its location in the protein sequence (See Figure 1 for the Cathepsin D protein). If you don't see the annotations or you wish to run the analysis again, click the "Sequence Signatures" link from the Tools panel, and the canonical sequence of the protein will be scanned. To run a particular sequence of the protein, go to the corresponding sequence page using the links in the Sequence Attributes section and follow the same steps described here.
See also: Help:Salivary Proteins, Help:Protein Annotation
Display of Results
Once the analysis is finished, the server at EBI returns the results to the wiki for display. For each signature detected, the location of the signature identified in the protein are shown graphically as in Figure 2 below. Of note is the score of each InterPro feature (with the location and evidence type). Clicking on the link to a given InterPro entry (highlighted) takes you to the respective Protein Signature page within the wiki.
References
| 1. | Quevillon E, et al. (2005) InterProScan: protein domains identifier. Nucleic Acids Res. 33(Web Server issue):W116-20 [PubMed:15980438] |
| 2. | Zdobnov EM and Apweiler R (2001) InterProScan--an integration platform for the signature-recognition methods in InterPro. Bioinformatics 17(9):847-8 [PubMed:11590104] |
