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Introduction

InterProScan is a tool that combines different protein signature recognition methods into one resource. InterProScan 5 is a re-implementation of the traditional InterProScan 4.x series and adds features such as pathway annotations and signal peptide and transmembrane prediction using Phobius.

Important Note

  • We kindly ask all users of EMBL-EBI Web Services to submit tool jobs in batches of no more than 30 at a time and not to submit more until the results and processing is complete. Please ensure that a valid email address is provided. Excessive usage of a particular resource will be dealt with in accordance with EMBL-EBI's Terms of Use. Please contact us if you need further information.

How to Access InterProScan 5

InterProScan 5 can be accessed via

Web Form

Web interface for InterProScan 5 is available at : http://www.ebi.ac.uk/interpro/

See http://www.ebi.ac.uk/interpro/faqs.html for more details.

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Web Services

Web Services are available using REST and SOAP protocols that enable programmatic access and allow their integration into other applications and analytical workflows and pipelines. 

For an introduction on how to run these clients and use them in workflows please see the webinar series.

REST API

The Representational State Transfer (REST) 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.

LanguageDownloadRequirements
Perliprscan5.plLWP and XML::Simple

Python

iprscan5.py

xmltramp2

For details see Environment setup for REST Web Services and Examples for Perl REST Web Services Clients pages.

WADL

The WADL for the InterProScan (REST) service: http://www.ebi.ac.uk/Tools/services/rest/iprscan5?wadl

Input

Sequences can be in any of the formats in the table below. Partially formatted sequences are not accepted. Adding a return to the end of the sequence may help certain applications understand the input. Note that using data directly from word processors may yield unpredictable results as hidden/control characters may be present. 

Nucleotide Sequences

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, 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://github.com/ebi-pf-team/interproscan for details. 


FormatProtein example
FASTA

UniProtKB/Swiss-Prot (abridged version)

Example    

Output

OrderProtein example
TSV
XMLExample
JSONExample 
GFF3Example 
SVGExample   

Tool parameters

Parameters

Command line parameter

Description

Values

Default

GO terms--gotermsSwitch on look-up of corresponding Gene Ontology annotationstrue / falsetrue
Pathways--pathwaysSwitch on look-up of corresponding pathway annotationstrue / falsetrue
Applications--applA number of different protein sequence applications are launched. These applications search against specific databases and have preconfigured cut off thresholdstrue / falsetrue

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SOAP API

The Simple Object Access Protocol (SOAP) 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.

WSDL

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


 List Methods
MethodsDescriptionArgumentsReturns

getParameters()

Get a list of the parameter names.nonea list of strings giving the names of the parameters.

getParameterDetails(parameterId)

Get details of a specific parameter.parameterId: identifier/name of the parameter to fetch details of.a wsParameterDetails describing the parameter and its values.

run(email, title, params)

Submit a job to the service.
  • 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.

a string containing the job identifier (jobId).

getStatus(jobId)

Get the status of a submitted job.jobId: (required) job identifier.

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.

getResultTypes(jobId)

Get the available result types for a finished job.jobId: (required) job identifier.a list of wsResultType data structures describing the available result types.

getResult(jobId, type, parameters)

Get the result of a job of the specified type.
  • 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.
 List Datatypes

InputParameters

The input parameters for the job:

AttributeTypeDescription
appllistSignature method applications to run.
gotermsbooleanEnable/disable inclusion of Gene Ontology (GO) terms in result.
pathwaysbooleanEnable/disable inclusion of pathways in result.
sequencestringProtein sequence to analyse. The use of fasta formatted sequence is recommended. The sequence data must not contain punctuation or stop ('*') characters.

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

wsParameterDetails

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

AttributeTypeDescription
namestringName of the parameter.
descriptionstringDescription of the parameter, suitable for use in option help interfaces.
typestringData type of the parameter.
valueslist of wsParameterValueList of valid values for the option.

wsParameterValue

Description of a tool parameter value. Used in wsParameterDetails.

AttributeTypeDescription
labelstringDisplay name of the value, for use in interfaces.
valuestringString representation of the value to be passed to the tool parameter.
defaultValuebooleanFlag indicating if this value is the default.
propertieslist of wsPropertyList of key/value pairs providing further information.

wsProperty

Properties of a tool parameter value. Used in wsParameterValue.

AttributeTypeDescription
keystringProperty name
valuestringProperty value

wsRawOutputParameter

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

AttributeTypeDescription
namestringParameter name
valuelist of stringParameter value

wsResultType

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

AttributeTypeDescription
identifierstringIdentifier for the result type. Passed as type to getResult(jobId, type, parameters).
labelstringDisplay name for use in user interfaces.
descriptionstringDescription of the result type, for use in help interfaces.
mediaTypestringMIME type of the returned data.
fileSuffixstringSuggested suffix for file name, if writing data to disk.

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Open API Interface

https://www.ebi.ac.uk/Tools/common/tools/help/index.html?tool=iprscan5


 List Endpoints

Endpoints

DescriptionArgumentsReturns

https://www.ebi.ac.uk/Tools/services/rest/iprscan5/parameters

Get a list of the parameter names.noneA list of strings giving the names of the parameters.

https://www.ebi.ac.uk/Tools/services/rest/iprscan5/parameterdetails/goterms

https://www.ebi.ac.uk/Tools/services/rest/iprscan5/parameterdetails/pathways

https://www.ebi.ac.uk/Tools/services/rest/iprscan5/parameterdetails/appl

https://www.ebi.ac.uk/Tools/services/rest/iprscan5/parameterdetails/sequence

Get details of a specific parameter.parameterdetail: identifier/name of the parameter to fetch details of.A wsParameterDetails describing the parameter and its values.

https://www.ebi.ac.uk/Tools/services/rest/iprscan5/run

Submit a job to the service.

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.

A string containing the job identifier (jobId).

https://www.ebi.ac.uk/Tools/services/rest/iprscan5/status/<jobid>


Get the status of a submitted job.jobId: (required) job identifier.

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: Job Dispatcher.

https://www.ebi.ac.uk/Tools/services/rest/iprscan5/resulttypes/<jobid>

Get the available result types for a finished job.

jobId: (required) job identifier.

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

https://www.ebi.ac.uk/Tools/services/rest/iprscan5/result/<jobid>/out

https://www.ebi.ac.uk/Tools/services/rest/iprscan5/result/<jobid>/log

https://www.ebi.ac.uk/Tools/services/rest/iprscan5/result/<jobid>/tsv

https://www.ebi.ac.uk/Tools/services/rest/iprscan5/result/<jobid>/xml

https://www.ebi.ac.uk/Tools/services/rest/iprscan5/result/<jobid>/htmltarball

https://www.ebi.ac.uk/Tools/services/rest/saps/result/<jobid>/gff

https://www.ebi.ac.uk/Tools/services/rest/saps/result/<jobid>/svg

https://www.ebi.ac.uk/Tools/services/rest/saps/result/<jobid>/sequence

https://www.ebi.ac.uk/Tools/services/rest/saps/result/<jobid>/json

Get the result of a job of the specified type.

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.

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Common Workflow Language

CWL (Common Workflow Language) implementation for consuming EMBL-EBI Bioinformatics Web Services tools' clients are available at https://github.com/ebi-wp/webservice-cwl

For details, see CWL Workflows page. 

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Reference 

InterProScan

EBI Web Services

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