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InterProScan 5 (REST)

Description

InterProScan 1) 2) 3) 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 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.


Chinese / 中文

敬告所有 EMBL-EBI Web Services 网络服务用户,请在呈交工具工作时,每批工作 不要超过30项,并请您在该批数据的结果和处理程序完成之后再呈交下一批工作。并请您提供一个有效的电子邮件地址。超额使用某项资源将按照 EMBL-EBI使用条款处理。 如需进一步信息,请通过此链接 与我们联系。


Korean / 한글

EMBL-EBI 웹서비스는 다량의 데이터(배치 등) 호출시, 사용자당 실시간으로 최대 30건의 처리를 제한적으로 사용하실 것을 권고드리고 있습니다. 보내신 건이 완료되기 전에, 재차 더 많은 데이터가 전송되지 않도록 협조 부탁드립니다. 또한 유효한 메일주소를 사용해주시기 바랍니다. 다량의 데이터 사용에 관한, EMBL-EBI 이용 약관을 준수해 주시것을 부탁드리며, 관련해 도움이 필요하시면, 문의 주시기 바랍니다.


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.

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
Java iprscan5.jar Java 8
Perl iprscan5_lwp.pl LWP and XML::Simple
Python iprscan5_urllib2.py urllib2 and xmltramp
Python3 iprscan5_urllib3.py urllib3, and xmltramp2
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.

WADL

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

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) Jones P, Binns D, Chang HY, Fraser M, Li W, McAnulla C, McWilliam H, Maslen J, Mitchell A, Nuka G, Pesseat S, Quinn AF, Sangrador-Vegas A, Scheremetjew M, Yong SY, Lopez R, Hunter S. (2014)
InterProScan 5: genome-scale protein function classification.
Bioinformatics. 30(9) 1236-1240.
PubMed: 24451626
DOI: 10.1093/bioinformatics/btu031.
2) 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
3) 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: 2017/02/16 09:55 by apc
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