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EBI_InterProScan_tmhmm_signalp

Workflow Entry: EBI_InterProScan_tmhmm_signalp

Created at: 26/10/08 @ 20:50:10 Last updated: 01/04/11 @ 08:56:37

Version 2 (of 4)

Version created on: 01/06/08 @ 11:21:45 by: Hamish McWilliam | Revision comments Expand

Last edited on: 01/06/08 @ 15:04:13 by: Hamish McWilliam

Title: EBI_InterProScan_tmhmm_signalp

Type: Taverna 1

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Description

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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http://www.myexperiment.org/workflows/212/download?version=2
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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. See the Service entry for this web service.
Get_text_result	arbitrarywsdl	Get the plain text format result. See the Service entry for this web service.
runInterProScan	arbitrarywsdl	Submit the InterProScan job. See the Service entry for this web service.
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 Original Uploader

Hamish McWilliam

Information License

All versions of this Workflow are licensed under:

Information Credits (1)

(People/Groups)

Hamish McWilliam

Information Attributions (1)

(Workflows/Files)

EBI_InterProScan

Information Tags (8)

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Information Shared with Groups (0)

None

Information Featured In Packs (1)

Private pack

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Information Ratings (0)

Current:

0.0 / 5

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Information Attributed By (1)

(Workflows/Files)

Protein_transmembrane_prediction

Information Favourited By (0)

No one

Information Statistics

2175 viewings

1237 downloads

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Citations (0)

None

Version History

Earliest Version:
[1] - EBI_InterProScan_tmhmm_signalp

Created on: Sunday 01 June 2008 @ 11:21:45 (GMT)

Created by: Hamish McWilliam

Last edited on: Sunday 01 June 2008 @ 11:21:46 (GMT)

Last edited by: Hamish McWilliam

Revision comments:

None

Previous Versions:
[2] - EBI_InterProScan_tmhmm_signalp

Created on: Sunday 01 June 2008 @ 11:21:45 (GMT)

Created by: Hamish McWilliam

Last edited on: Sunday 01 June 2008 @ 15:04:13 (GMT)

Last edited by: Hamish McWilliam

Revision comments:

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

[3] - EBI_InterProScan_tmhmm_signalp

Created on: Sunday 01 June 2008 @ 11:21:45 (GMT)

Created by: Hamish McWilliam

Last edited on: Sunday 01 June 2008 @ 15:05:36 (GMT)

Last edited by: Hamish McWilliam

Revision comments:

Latest Version:
[4] - EBI_InterProScan_tmhmm_signalp

Created on: Sunday 26 October 2008 @ 20:50:10 (GMT)

Created by: Hamish McWilliam

Last edited on: Friday 01 April 2011 @ 08:56:37 (GMT)

Last edited by: Hamish McWilliam

Revision comments:

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

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Other workflows that use similar services (17)

Only the first 2 workflows that use similar services are shown. View all workflows that use these services.

Taverna 2

Original Uploader

Stian Soiland-Reyes

EBI_InterProScan for Taverna 2 (v2)

Created: 26/01/10 @ 14:46:07 | Last updated: 26/01/10 @ 14:46:08

Credits: Stian Soiland-Reyes Paolo Katy Wolstencroft Hamish McWilliam

Attributions: EBI InterproScan T2 EBI_InterProScan

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Perform an InterProScan analysis of a protein sequence using the EBI’s WSInterProScan service (see http://www.ebi.ac.uk/Tools/webservices/services/interproscan). The input sequence to use and the user e-mail address are inputs, the other parameters for the analysis (see Job_params) are allowed to default. InterProScan searches a protein sequence against the protein family and domain signature databases integrated into InterPro (see http://www.ebi.ac.uk/interpro/). A set of matches to the sig...

Rating: 0.0 / 5 (0 ratings) | Versions: 2 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 175 times | Downloaded: 122 times

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