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InterProScan 5 (REST)

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
Perl iprscan5_lwp.pl LWP and XML::Simple
Python iprscan5_urllib2.py urllib, urllib2 and xmltramp
Ruby iprscan5_net_http.rb net/http and REXML

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

Resources

parameters

List parameter names.

Request

URL http://www.ebi.ac.uk/Tools/services/rest/iprscan5/parameters/
Parameters none

Response

An XML document containing a list of parameter names.

For example: http://www.ebi.ac.uk/Tools/services/rest/iprscan5/parameters/

parameterdetails

Get detailed information about a parameter.

Request

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

run

Submit a job with the specified parameters.

Request

URL http://www.ebi.ac.uk/Tools/services/rest/iprscan5/run/
POST email User e-mail address. See Why do you need my e-mail address?
title an optional title for the job.
appl list of signature methods to run
goterms enable/disable Gene Ontology terms in result
pathways enable/disable pathways in result
sequence 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 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/iprscan5/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 Synchronous and Asynchronous Access: JDispatcher.

resulttypes

Get available result types for a finished job.

Request

URL http://www.ebi.ac.uk/Tools/services/rest/iprscan5/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/iprscan5/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.

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_rest.txt · Last modified: 2014/04/11 12:41 by hpm
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