InterProScan 5
Introduction
InterProScan is a tool that combines different protein signature recognition methods into one resource. The number of signature databases and their associated scanning tools, as well as the further refinement procedures, increases the complexity of the problem.
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How to use this tool
Running a tool from the web form is a simple multiple steps process, starting at the top of the page and following the steps to the bottom.
Each tool has at least 2 steps, but most of them have more:
- The first steps are usually where the user sets the tool input (e.g. sequences, databases...)
- In the following steps, the user has the possibility to change the default tool parameters
- And finally, the last step is always the tool submission step, where the user can specify a title to be associated with the results and an email address for email notification. Using the submit button will effectively submit the information specified previously in the form to launch the tool on the server
Note that the parameters are validated prior to launching the tool on the server and in the event of a missing or wrong combination of parameters, the user will be notified directly in the form.
Step 1 - Input Sequence
Sequence Input Window
Your protein sequence can be entered directly into this form in GCG, FASTA, EMBL, PIR, NBRF or UniProtKB/Swiss-Prot format. A partially formatted sequence is not accepted. Adding a return to the end of the sequence may help certain applications understand the input. Note that directly using data from word processors may yield unpredictable results as hidden/control characters may be present.
Sequence File Upload
A file containing valid protein sequence in any format (GCG, FASTA, EMBL, PIR, NBRF or UniProtKB/Swiss-Prot format) can be used as input for the search. Word processors files may yield unpredictable results as hidden/control characters may be present in the files. It is best to save files with the Unix format option to avoid hidden Windows characters.
Step 2 - Select Applications
Application
A number of different protein sequence applications are launched. These applications search against specific databases and have preconfigured cut off thresholds.
| Program Name | Description | Abbreviation |
|---|---|---|
| BlastProDom | Scans the families in the ProDom database. ProDom is a comprehensive set of protein domain families automatically generated from the UniProtKB/Swiss-Prot and UniProtKB/TrEMBL sequence databases using psi-blast. In InterProScan the blastpgb program is used to scan the database. BLASTPGP performs gapped blastp searches and can be used to perform iterative searches in PSI-BLAST and PHI-BLAST mode. | ProDom |
| FPrintScan | Scans against the fingerprints in the PRINTS database. These fingerprints are groups of motifs that together are more potent than single motifs by making use of the biological context inherent in a multiple motif method. | PRINTS |
| HMMPIR | Scans the hidden markov models (HMMs) that are present in the PIR Protein Sequence Database (PSD) of functionally annotated protein sequences, PIR-PSD. | PIRSF |
| HMMPfam | Scans the hidden markov models (HMMs) that are present in the PFAM Protein families database. | PfamA |
| HMMSmart | Scans the hidden markov models (HMMs) that are present in the SMART domain/domain families database. | SMART |
| HMMTigr | Scans the hidden markov models (HMMs) that are present in the TIGRFAMs protein families database. | TIGRFAM |
| ProfileScan | Scans against PROSITE profiles. These profiles are based on weight matrices and are more sensitive for the detection of divergent protein families. | PrositeProfiles |
| HAMAP | Scans against HAMAP profiles. These profiles are based on weight matrices and are more sensitive for the detection of divergent bacterial, archaeal and plastid-encoded protein families. | HAMAP |
| PatternScan | PatternScan is a new version of the PROSITE pattern search software which uses new code developed by the PROSITE team. | PrositePatterns |
| SuperFamily | SUPERFAMILY is a library of profile hidden Markov models that represent all proteins of known structure. | SuperFamily |
| HMMPanther | Panther | |
| Gene3D | Gene3d | |
| Coils | Coils | |
| CDD | CDD |
Default value is: CDD
Step 3 - Submission
Job title
It's possible to identify the tool result by giving it a name. This name will be associated to the results and might appear in some of the graphical representations of the results.
Email Notification
Running a tool is usually an interactive process, the results are delivered directly to the browser when they become available. Depending on the tool and its input parameters, this may take quite a long time. It's possible to be notified by email when the job is finished by simply ticking the box "Be notified by email". An email with a link to the results will be sent to the email address specified in the corresponding text box. Email notifications require valid email addresses.
Email Address
If email notification is requested, then a valid Internet email address must be provided. This is not required when running the tool interactively (The results will be delivered to the browser window when they are ready).