From 15th February 2011 the WSInterProScan service used by these clients is deprecated and no longer maintained. On Monday 28th March 2011 the service will be decommissioned.

The WSInterProScan service is replaced by the following services:

• InterProScan (REST)
• InterProScan (SOAP)

We recommend that all users migrate their usage to the new services and corresponding clients as soon as possible.

The documentation and clients below are historical and provided solely for reference purposes.

InterProScan is a tool that combines different protein signature recognition methods native to the InterPro member databases into one resource with look up of corresponding InterPro and GO annotation. This service allows you to query your protein sequence against InterPro.

For more information about this tool see:

• EBI Tools:
  • InterProScan
• Stand-alone InterProScan
  • Readme
  • FAQs
• InterPro
  • User manual
  • Help pages

We kindly ask all users of SOAP Web Services to submit jobs in batches of up to 25 sequences at a time and to not submit more until the results and processing has completed for these. This should enable the users as well as the EBI 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 EBI's Terms of Use.

Due to resource limitations the InterProScan service no longer accepts nucleotide sequence submissions.

To process nucleotide sequences using InterProScan:

1. Translate your nucleotide sequence
The standalone version of InterProScan uses EMBOSS sixpack to perform the translation and filter the resulting open reading frame (ORF) sequences by length. Alternative tools such as EMBOSS getorf and EMBOSS transeq can also be used, 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 our EMBOSS webservices, SOAPlab and as part of the EMBOSS package.

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 sixpack and EMBOSS getorf tools provide an option 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, you can go directly to the InterPro Matches databases to get the signature matches for the sequence.

Note: the standalone version of InterProScan 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 InterProScan Readme for details.

For details of the service used by these clients see WSInterProScan.

The Microsoft .NET runtime is already installed on most MS Windows systems. The Microsoft .NET runtime is available via Microsoft Update or as a download (see http://msdn.microsoft.com/netframework/).

For MacOS X, Linux and other non-Windows systems see Mono or DotGNU.

Download the C# client:

• Executable: wsinterproscan.exe
• Source code: wsinterproscan.cs

Run without arguments to get a usage summary:

wsinterproscan.exe

Download and unzip the library files lib-1.4.zip and add the jars to the Java classpath.

Download the Java client:

• Executable: WSInterProScan.jar
• Source code: WSInterProScanClient.java

To get usage information run the client without arguments:

java -Djava.ext.dirs=lib -jar WSInterProScan.jar

To run the Perl client you need to install SOAP::Lite. SOAP::Lite is a collection of Perl modules which provides a simple and lightweight interface to SOAP both on client and server side. This client requires SOAP::Lite version 0.60.

Download the Perl client: interproscan.pl

To get usage information run without arguments:

perl interproscan.pl

A number of other example clients are available in a range of languages:

• PHP (tutorial)
  • nuSOAP: wsinterproscan_cli_nusoap.php
  • PHP SOAP: wsinterproscan_cli_php_soap.php
• Python (tutorial)
  • Using SOAPpy: wsinterproscan.py
• Ruby (tutorial)
  • Using SOAP4r: wsinterproscan.rb
• Visual Basic .NET (tutorial)
  • Executable: wsinterproscan.exe
  • Source: wsinterproscan.vb

Workflow engines such as Taverna and Triana offer a simple way of combining individual web services into complex applications.

A number of workflows are available on myExperiment. For example:

• EBI_InterProScan: a basic workflow showing how to use WSInterProScan in Taverna.
• Nucleotide_InterProScan: a more complex workflow to perform InterProScan on nucleotide sequences.