EMBL-EBI Web Services

This page is read only. You can view the source, but not change it. Ask your administrator if you think this is wrong.
====== InterProScan 4.x (REST) ======

===== Description =====

InterProScan ((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: [[http://europepmc.org/abstract/MED/15980438|15980438]]\\ 
DOI: [[http://dx.doi.org/10.1093/nar/gki442|10.1093/nar/gki442]]\\ 
)) ((Zdobnov E.M. and Apweiler R. (2001)\\
**InterProScan--an integration platform for the signature-recognition methods in InterPro.**\\
Bioinformatics 17(9):847-848\\
PubMed: [[http://europepmc.org/abstract/MED/11590104|11590104]]\\
DOI: [[http://dx.doi.org/10.1093/bioinformatics/17.9.847|10.1093/bioinformatics/17.9.847]]
)) is a tool that combines different protein signature recognition methods into one resource.

**Note**: this service uses InterProScan 4.x, for details about the currently available versions of InterProScan please see: [[ftp://ftp.ebi.ac.uk/pub/software/unix/iprscan/index.html]].

For more information see:
  * Web form: [[http://www.ebi.ac.uk/Tools/pfa/iprscan/]]
  * [[.:iprscan_soap|Document/literal SOAP service]]
  * InterProScan 4.x package:
    * [[ftp://ftp.ebi.ac.uk/pub/software/unix/iprscan/4/README.html|README]]
    * [[ftp://ftp.ebi.ac.uk/pub/software/unix/iprscan/4/FAQs.html|FAQ]]

Web service registry entries:
  * [[http://www.biocatalogue.org/services/2769|BioCatalogue]]
  * [[http://health2api.com/?p=9496|Health 2.0 API]]
  * [[http://www.programmableweb.com/api/ebi-interproscan|ProgrammableWeb.com]]

===== Important ====

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 [[http://www.ebi.ac.uk/about/terms-of-use|EMBL-EBI's Terms of Use]].

If you are planning on systematically processing many sequences using this service please see [[:help:interproscan|InterProScan Web Service FAQ]].

==== Nucleotide Sequences ====

To process nucleotide sequences using InterProScan 4.x:

  - **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 [[http://emboss.open-bio.org/rel/rel6/apps/sixpack.html|EMBOSS sixpack]] to perform the translation and filter the resulting open reading frame (ORF) sequences by length. Alternative tools such as [[http://emboss.open-bio.org/rel/rel6/apps/transeq.html|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 [[http://emboss.open-bio.org/|EMBOSS]] package, and via the [[:about:webservices#sequence_translation|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.
  - **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 [[http://emboss.open-bio.org/|EMBOSS]] programs [[http://emboss.open-bio.org/rel/rel6/apps/getorf.html|getorf]] and [[http://emboss.open-bio.org/rel/rel6/apps/sixpack.html|sixpack]] provide options to do length filtering when performing the translation.
  - **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 [[http://www.uniprot.org/help/uniprotkb|UniProtKB]] or [[http://www.uniprot.org/help/uniparc|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 [[http://www.ebi.ac.uk/Tools/picr/|PICR]] or [[http://www.ebi.ac.uk/Tools/so/seqcksum/|SeqCksum]]), you can go directly to the InterPro Matches databases to get the signature matches for the sequence (available in [[http://www.ebi.ac.uk/Tools/dbfetch/|dbfetch]] and [[:services:dbfetch|WSDbfetch]] as [[http://www.ebi.ac.uk/Tools/dbfetch/dbfetch/dbfetch.databases#iprmc|IPRMC]] or [[http://www.ebi.ac.uk/Tools/dbfetch/dbfetch/dbfetch.databases#iprmcuniparc|IPRMC UniParc]], in the [[http://www.ebi.ac.uk/interpro/biomart/martview/|InterPro BioMart]] or on the [[ftp://ftp.ebi.ac.uk/pub/databases/interpro/|InterPro FTP site]]).

**Note**: the standalone version of InterProScan 4.x 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 [[ftp://ftp.ebi.ac.uk/pub/software/unix/iprscan/4/README.html|InterProScan 4.x Readme]] 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 ^
^ Perl | ''[[http://www.ebi.ac.uk/Tools/webservices/download_clients/perl/lwp/iprscan_lwp.pl|iprscan_lwp.pl]]'' | [[http://search.cpan.org/perldoc?LWP|LWP]] and [[http://search.cpan.org/perldoc?XML::Simple|XML::Simple]] |
^ Python | ''[[http://www.ebi.ac.uk/Tools/webservices/download_clients/python/urllib/iprscan_urllib2.py|iprscan_urllib2.py]]'' | [[http://www.python.org/doc/lib/module-urllib.html|urllib]], [[http://www.python.org/doc/lib/module-urllib2.html|urllib2]] and [[http://www.aaronsw.com/2002/xmltramp/|xmltramp]] |
^ Ruby | ''[[http://www.ebi.ac.uk/Tools/webservices/download_clients/ruby/net_http/iprscan_net_http.rb|iprscan_net_http.rb]]'' | [[http://www.ruby-doc.org/stdlib/libdoc/net/http/rdoc/index.html|net/http]] and [[http://ruby-doc.org/stdlib/libdoc/rexml/rdoc/index.html|REXML]] |

For further details of these tool-kits and workflow platforms see our [[:tutorials:00_Contents|Guide to Web Services]].

===== Resources =====

==== parameters ====

List parameter names.

**Request**

^ URL         | http://www.ebi.ac.uk/Tools/services/rest/iprscan/parameters/ |
^ Parameters  | //none// |

**Response**

An XML document containing a list of parameter names.

For example: http://www.ebi.ac.uk/Tools/services/rest/iprscan/parameters/

==== parameterdetails ====

Get detailed information about a parameter.

**Request**

^ URL         | http://www.ebi.ac.uk/Tools/services/rest/iprscan/parameterdetails/$parameterId |
^ Parameters  | ''$parameterId'': the name of the parameter |

**Response**

An XML document providing details about the parameter.

For example: http://www.ebi.ac.uk/Tools/services/rest/iprscan/parameterdetails/appl.

==== run ====

Submit a job with the specified parameters.

**Request**

^ URL         | http://www.ebi.ac.uk/Tools/services/rest/iprscan/run/ ||
^ POST        | ''email''        | User e-mail address. See [[help:faq#why_do_you_need_my_e-mail_address|Why do you need my e-mail address?]] |
^             | ''title''        | an optional title for the job. |
^             | ''[[http://www.ebi.ac.uk/Tools/services/rest/iprscan/parameterdetails/appl|appl]]''         | list of signature methods to run |
^             | ''[[http://www.ebi.ac.uk/Tools/services/rest/iprscan/parameterdetails/goterms|goterms]]''      | enable/disable Gene Ontology terms in result |
^             | ''[[http://www.ebi.ac.uk/Tools/services/rest/iprscan/parameterdetails/nocrc|nocrc]]''        | enable/disable sequence CRC look-up in InterPro matches |
^             | ''[[http://www.ebi.ac.uk/Tools/services/rest/iprscan/parameterdetails/sequence|sequence]]''     | Protein sequence to analyse. The use of fasta formatted sequence is recommended. |

More detailed information about each parameter, including valid values can be obtained using the [[#parameterdetails]] resource.

**Response**

A plain text document containing the job identifier.

==== status ====

Get the status of a submitted job.

**Request**

^ URL         | http://www.ebi.ac.uk/Tools/services/rest/iprscan/status/$jobId |
^ Parameters  | ''$jobId'': job identifier |

**Response**

A plain text document containing the job 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 [[:tutorials:01_intro#jdispatcher|Synchronous and Asynchronous Access: JDispatcher]].

==== resulttypes ====

Get available result types for a finished job.

**Request**

^ URL         | http://www.ebi.ac.uk/Tools/services/rest/iprscan/resulttypes/$jobId |
^ Parameters  | ''$jobId'': job identifier |

**Response**

An XML document detailing the available result types.

==== result ====

Get the job result of the specified type.

**Request**

^ URL         | http://www.ebi.ac.uk/Tools/services/rest/iprscan/result/$jobId/$resultType |
^ Parameters  | ''$jobId'': job identifier |
^             | ''$resultType'': type of result to retrieve. See [[#resulttypes]]. |

**Response**

A document containing the result in the requested format. The MIME type of the returned document is set according to the format.
EMBL-EBI Web Services

EMBL-EBI

Services

Research

Training

Industry

About us
