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InterProScan 5 (SOAP)

Description

InterProScan 1) 2) is a tool that combines different protein signature recognition methods into one resource. InterProScan 5 is a reimplementation of the traditional InterProScan 4.x series and adds features such as pathway annotations and signal peptide and transmembrane prediction using Phobius.

For more information see:

Important

We kindly ask all users of EMBL-EBI Web Services to submit tool jobs in batches of up to 30 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.

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, 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.

Clients

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.

Language Download Requirements
C# .NET Executable: IPRScan5CliClient.exe; Source: AbstractWsClient.cs, IPRScan5Client.cs, IPRScan5CliClient.cs A .NET runtime environment. If building from source development tools are also required. See the .NET tutorial for details.
Java Executable jar: IPRScan5_Axis1.jar; Source: AbstractWsToolClient.java, IPRScan5Client.java Axis 1.4; All dependencies, including Axis 1.4 and Commons-CLI, are available in ebiws-lib.zip.
Executable jar: IPRScan5_JAXWS.jar; Source: AbstractWsToolClient.java, IPRScan5Client.java JAX-WS; Various dependencies including Commons-CLI, are available in ebiws-lib.zip.
Perl iprscan5_soaplite.pl SOAP::Lite
iprscan5_xmlcompile.pl XML::Compile::SOAP
PHP iprscan5_lib_php_soap.php, iprscan5_cli_php_soap.php, iprscan5_web_php_soap.php PHP-SOAP
Python iprscan5_soappy.py SOAPpy
iprscan5_suds.py suds
Ruby iprscan5_soap4r.rb soap4r

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

WSDL

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

Operations

getParameters()

Get a list of the parameter names.

Arguments: none

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

getParameterDetails(parameterId)

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.

run(email, title, params)

Submit a job to the service.

Arguments:

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

getStatus(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.

getResultTypes(jobId)

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.

getResult(jobId, type, parameters)

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.

Data Types

InputParameters

The input parameters for the job:

Attribute Type Description
appl list Signature method applications to run.
goterms boolean Enable/disable inclusion of Gene Ontology (GO) terms in result.
pathways boolean Enable/disable inclusion of pathways in result.
sequence string Protein 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).

Attribute Type Description
name string Name of the parameter.
description string Description of the parameter, suitable for use in option help interfaces.
type string Data type of the parameter.
values list of wsParameterValue List of valid values for the option.

wsParameterValue

Description of a tool parameter value. Used in wsParameterDetails.

Attribute Type Description
label string Display name of the value, for use in interfaces.
value string String representation of the value to be passed to the tool parameter.
defaultValue boolean Flag indicating if this value is the default.
properties list of wsProperty List of key/value pairs providing further information.

wsProperty

Properties of a tool parameter value. Used in wsParameterValue.

Attribute Type Description
key string
value string

wsRawOutputParameter

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

Attribute Type Description
name string
value list of string

wsResultType

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

Attribute Type Description
identifier string Identifier for the result type. Passed as type to getResult(jobId, type, parameters).
label string Display name for use in user interfaces.
description string Description of the result type, for use in help interfaces.
mediaType string MIME type of the returned data.
fileSuffix string Suggested suffix for file name, if writing data to disk.
1) Quevillon E., Silventoinen V., Pillai S., Harte N., Mulder N., Apweiler R. and Lopez R. (2005)
InterProScan: protein domains identifier.
Nucleic Acids Res. 33:W116-20
PubMed: 15980438
DOI: 10.1093/nar/gki442
2) Zdobnov E.M. and Apweiler R. (2001)
InterProScan–an integration platform for the signature-recognition methods in InterPro.
Bioinformatics 17(9):847-848
PubMed: 11590104
DOI: 10.1093/bioinformatics/17.9.847
 
services/pfa/iprscan5_soap.txt · Last modified: 2014/04/11 12:01 by hpm
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