EBI_InterProScan_tmhmm_signalp

Created: 2008-10-26 20:50:10 Last updated: 2011-04-01 08:56:37

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Use the TMHMM and SignalP methods of InterProScan to perform transmembrane and signal peptide prediction. The EBI's InterProScan web service (see http://www.ebi.ac.uk/Tools/webservices/services/interproscan) is used.

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Workflow Components

Inputs (2)

Name	Description
Email_address	User e-mail address
Sequence_or_ID	Input protein sequence for analysis. This can either be the actual sequence (fasta format recommended) or a database identifier in database:identifer format (e.g. uniprot:LPHN2_RAT).

Processors (10)

Name	Type	Description
Unpack_XML_result	local	Unpack byte[] version of result into a string.
Job_params	local	InterProScan job parameters.
Get_XML_result	arbitrarywsdl	Get the XML format result.
Get_text_result	arbitrarywsdl	Get the plain text format result.
runInterProScan	arbitrarywsdl	Submit the InterProScan job.
Input_data	local	Populate input data structure with input sequence and data type.
Content_list	local	Wrap input data in a list.
Unpack_text_result	local	Unpack byte[] version of result into a string.
EBI_InterProScan_poll_job	workflow	Wait for the job to complete.
Format_as_GFF	beanshell

Beanshells (2)

Name	Description	Inputs	Outputs
Is_done	Map status codes into true/false is done flag.	job_status	is_done
Format_as_GFF		interproscan_text_result	gff_result

Outputs (4)

Name	Description
InterProScan_text_result	InterProScan result in tab delimited plain text format.
InterProScan_XML_result	InterProScan result in XML format.
Job_ID	EBI job identifier.
GFF_result

Links (15)

Source	Sink
Content_list:output	runInterProScan:content
Email_address	Job_params:email
Get_XML_result:output	Unpack_XML_result:bytes
Get_text_result:output	Unpack_text_result:bytes
Input_data:output	Content_list:WSArrayofData
Job_params:output	runInterProScan:params
Sequence_or_ID	Input_data:content
Format_as_GFF:gff_result	GFF_result
Unpack_text_result:string	Format_as_GFF:interproscan_text_result
Unpack_text_result:string	InterProScan_text_result
runInterProScan:jobid	EBI_InterProScan_poll_job:Job_ID
runInterProScan:jobid	Get_XML_result:jobid
runInterProScan:jobid	Get_text_result:jobid
Unpack_XML_result:string	InterProScan_XML_result
runInterProScan:jobid	Job_ID

Coordinations (2)

Controller	Target
EBI_InterProScan_poll_job	Get_text_result
EBI_InterProScan_poll_job	Get_XML_result

Information Workflow Type

Taverna 1

Information Uploader

Hamish McWilliam

Information License

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Information Version 2 (of 4)

Information Credits (1)

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Hamish McWilliam

Information Attributions (1)

(Workflows/Files)

EBI_InterProScan

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Information Attributed By (1)

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Protein_transmembrane_prediction

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Information Statistics

7150 viewings

2982 downloads

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Citations (0)

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Version History

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EBI_InterProScan_tmhmm_signalp

Created by Hamish McWilliam on Sunday 01 June 2008 11:21:45 (UTC)

Last edited by Hamish McWilliam on Sunday 01 June 2008 11:21:46 (UTC)
EBI_InterProScan_tmhmm_signalp

Created by Hamish McWilliam on Sunday 01 June 2008 11:21:45 (UTC)

Last edited by Hamish McWilliam on Sunday 01 June 2008 15:04:13 (UTC)

Revision comment:

Add GFF (see http://www.sanger.ac.uk/Software/formats/GFF/) style output option.
EBI_InterProScan_tmhmm_signalp

Created by Hamish McWilliam on Sunday 01 June 2008 11:21:45 (UTC)

Last edited by Hamish McWilliam on Sunday 01 June 2008 15:05:36 (UTC)

Revision comment:
EBI_InterProScan_tmhmm_signalp

Created by Hamish McWilliam on Sunday 26 October 2008 20:50:10 (UTC)

Last edited by Hamish McWilliam on Friday 01 April 2011 08:56:37 (UTC)

Revision comment:

Update for change in the poll operations output names in the web service description.

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Note: the WSInterProScan web service used by this workflow is no longer available haveing been replaced by the EMBL-EBI's InterProScan (REST) (http://www.ebi.ac.uk/Tools/webservices/services/pfa/iprscan_rest) and InterProScan (SOAP) (http://www.ebi.ac.uk/Tools/webservices/services/pfa/iprscan_soap) web services. Thus the workflow described here no longer works, see the alternative workflows for the InterProScan (SOAP) service for workflows which use the new services. Perform an InterProScan ...

Created: 2008-10-26 | Last updated: 2011-04-01

Credits: Hamish McWilliam