InterProScan ^{1) 2)} is a tool that combines different protein signature recognition methods into one resource.

Note: this service uses InterProScan 5 RC7, for details about the currently available versions of InterProScan please see: https://code.google.com/p/interproscan.

For more information see:

• Web form: http://www.ebi.ac.uk/interpro/
• REST service
• InterProScan 5 web site at Google Code: https://code.google.com/p/interproscan
  • InterProScan 5 software documentation: https://code.google.com/p/interproscan/wiki/Introduction

We kindly ask all users of EMBL-EBI Web Services to submit tool jobs in batches of up to 25 at a time and to not submit more until the results and processing has completed for these. This enables users as well as the service maintainers to deal more easily with local and remote network outages as well as scheduled or unscheduled downtime.

Service provision happens on a fair-share basis. Overzealous usage of a particular resource will be dealt with in accordance to the EMBL-EBI's Terms of Use.

If you are planning on systematically processing many sequences using this service please see InterProScan Web Service FAQ for more ideas.

To process nucleotide sequences using InterProScan 5:

1. Translate your nucleotide sequence. The standalone version of InterProScan 4.x uses a basic ORF finding process to predict possible proteins for a nucleotide sequence. This uses EMBOSS sixpack to perform the translation and filter the resulting open reading frame (ORF) sequences by length. Alternative tools such as EMBOSS transeq are also available, but may require an additional filtering process to limit the ORF sequences to those above a certain length. These tools are available as part of the EMBOSS package, and via the Sequence Translation web services. For organisms where transcripts are spliced before translation, the use of more sophisticated gene prediction software is recommended to obtain probable protein sequences for the genes found.
2. Filter ORFs by sequence length. Short sequences (<80 aa) are unlikely to have any signature matches, so unless there is additional evidence that the sequence occurs, short sequences can be discarded. The EMBOSS programs getorf and sixpack provide options to do length filtering when performing the translation.
3. Significant hits from sequence similarity searches. The signatures used by InterProScan are based on known protein sequences so a filtering step by performing a BLAST or FASTA sequence similarity search with the ORF translations against the UniProtKB or UniParc protein sequence databases and only keeping sequences which have hits with E-values <0.001. In the case where an exact match is found to the sequence (using a sequence similarity search or services such as PICR or SeqCksum), you can go directly to the InterPro Matches databases to get the signature matches for the sequence (available in dbfetch and WSDbfetch as IPRMC or IPRMC UniParc, in the InterPro BioMart or on the InterPro FTP site).

Note: the standalone version of InterProScan 5 can perform the translation and ORF length filtering as part of the submission and is recommended if you need to perform large numbers of analysis and have access to the required resources. See https://code.google.com/p/interproscan for details.

Sample clients are provided for a number of programming languages. For details of how to use these clients, download the client and run the program without any arguments.

For further details of these tool-kits and workflow platforms see our Guide to Web Services.

The WSDL for the InterProScan SOAP service: http://www.ebi.ac.uk/Tools/services/soap/iprscan5?wsdl

Get a list of the parameter names.

Arguments: none

Returns: a list of strings giving the names of the parameters.

Get details of a specific parameter.

Arguments:

• parameterId: identifier/name of the parameter to fetch details of.

Returns: a wsParameterDetails describing the parameter and its values.

Submit a job to the service.

Arguments:

• email: (required) user e-mail address. See Why do you need my e-mail address?
• title: job title. Default: ””.
• params: (required) parameters for the tool. These are described by the InputParameters data structure.

Returns: a string containing the job identifier (jobId).

Get the status of a submitted job.

Arguments:

• jobId: (required) job identifier.

Returns: a string containing the status.

The values for the status are:

• RUNNING: the job is currently being processed.
• FINISHED: job has finished, and the results can then be retrieved.
• ERROR: an error occurred attempting to get the job status.
• FAILURE: the job failed.
• NOT_FOUND: the job cannot be found.

Further details can be found in Synchronous and Asynchronous Access: JDispatcher.

Get the available result types for a finished job.

Arguments:

• jobId: (required) job identifier.

Returns: a list of wsResultType data structures describing the available result types.

Get the result of a job of the specified type.

Arguments:

• jobId: (required) job identifier.
• type: (required) string specifying the result type to fetch. See getResultTypes(jobId) for details of the available types.
• parameters: optional list of wsRawOutputParameter used to provide additional parameters for derived result types.

Returns: the result data for the specified type, base64 encoded. Depending on the SOAP library and programming language used the result may be returned in decoded form. For some result types (e.g. images) this will be binary data rather than a text string.

The input parameters for the job:

More detailed information about each parameter, including valid values can be obtained using the getParameterDetails(parameterId) operation.

Descriptive information about a tool parameter. Returned by getParameterDetails(parameterId).

Description of a tool parameter value. Used in wsParameterDetails.

Properties of a tool parameter value. Used in wsParameterValue.

Additional parameters passed when requesting a result. See getResult(jobId, type, parameters).

Description of a result type. Returned by getResultTypes(jobId).