InterProScan 5


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


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
SignalPHMM SignalP
HMMPanther Panther
Gene3D Gene3d
Phobius Phobius
Coils Coils

Default value is: Coils

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 in the form 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).


InterProScan 5: genome-scale protein function classification.
(2014 May 01) Bioinformatics (Oxford, England) 30 (9) :1236-40
InterProScan: protein domains identifier.
(2005 July 01) Nucleic acids research 33 (Web Server issue) :W116-20
InterProScan--an integration platform for the signature-recognition methods in InterPro.
(2001 September) Bioinformatics (Oxford, England) 17 (9) :847-8
The EMBL-EBI bioinformatics web and programmatic tools framework.
(2015 July 01) Nucleic acids research 43 (W1) :W580-4
Analysis Tool Web Services from the EMBL-EBI.
(2013 July) Nucleic acids research 41 (Web Server issue) :W597-600