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EBI_Phobius

Workflow Entry: EBI_Phobius

Created at: 01/06/08 @ 11:08:45 Last updated: 02/06/08 @ 21:39:06

Version 2 (latest) (of 2)

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

Last edited on: 02/06/08 @ 21:39:06 by: Hamish McWilliam

Title: EBI_Phobius

Type: Taverna 1

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Description

The Phobius tool predicts transmembrane domains and signal peptide region from a protein sequence. This workflow uses the EBI's WSPhobius web service (see http://www.ebi.ac.uk/Tools/webservices/services/phobius) to access the tool. The predicted features are returned in a UniProtKB style feature listing.

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Option 1:

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Option 2:

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http://www.myexperiment.org/workflows/211/download?version=2
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Workflow Components

Inputs (2)

Name	Description
Email	User e-mail address.
Sequence_or_ID	Protein sequence to analyse. Either the actual sequence (fasta format recommended) or an entry identifer in database:identifer format (e.g. uniprot:LPHN2_RAT).

Processors (8)

Name	Type	Description
Contents_list	local	Wrap input data in a list.
runPhobius	arbitrarywsdl	Submit a Phobius analysis job (see http://www.ebi.ac.uk/Tools/webservices/services/phobius#runphobius_params_content) See the Service entry for this web service.
Job_params	local	Parameters for the job. Set to give UniProtKB style features as output.
Input_data	local	Add a type to the input data.
Unpack_text_output	local	Unpack byte[] recived into a string.
Get_text_result	arbitrarywsdl	Wait until the job has finished and get the specified type of result data. (see http://www.ebi.ac.uk/Tools/webservices/services/phobius#poll_jobid_type) See the Service entry for this web service.
EBI_Phobius_poll_job	workflow	Check for job completion.
Format_as_GFF	beanshell

Beanshells (2)

Name	Description	Inputs	Outputs
Is_done		job_status	is_done
Format_as_GFF		phobius_output	phobius_gff

Outputs (3)

Name	Description
Job_ID	EBI job identifier.
Phobius_output	Predicted features in a UniProtKB style format.
Phobius_GFF

Links (12)

Source	Sink
Contents_list:output	runPhobius:content
Email	Job_params:email
Format_as_GFF:phobius_gff	Phobius_GFF
Get_text_result:output	Unpack_text_output:bytes
Input_data:output	Contents_list:WSArrayofData
Sequence_or_ID	Input_data:content
Job_params:output	runPhobius:params
Unpack_text_output:string	Format_as_GFF:phobius_output
Unpack_text_output:string	Phobius_output
runPhobius:jobid	EBI_Phobius_poll_job:Job_ID
runPhobius:jobid	Get_text_result:jobid
runPhobius:jobid	Job_ID

Coordinations (1)

Controller	Target
EBI_Phobius_poll_job	Get_text_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 (0)

(Workflows/Files)

None

Information Tags (8)

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Information Shared with Groups (0)

None

Information Featured In Packs (2)

Private pack
EMBL-EBI Web Services (retired)

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Information Ratings (0)

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Information Attributed By (1)

(Workflows/Files)

Protein_transmembrane_prediction

Information Favourited By (0)

No one

Information Statistics

1148 viewings

1083 downloads

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Citations (0)

None

Version History

In chronological order:

EBI_Phobius

Created by Hamish McWilliam on Sunday 01 June 2008 @ 11:08:45 (UTC)
EBI_Phobius

Created by Hamish McWilliam on Sunday 01 June 2008 @ 11:08:45 (UTC)

Last edited by Hamish McWilliam on Monday 02 June 2008 @ 21:39:06 (UTC)

Revision comment:

Add GFF output.

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Other workflows that use similar services (1)

Taverna 1

Original Uploader

Hamish McWilliam

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Download (v2)

Protein_transmembrane_prediction (2)

Created: 26/10/08 @ 21:16:10 | Last updated: 01/04/11 @ 08:57:10

Credits: Hamish McWilliam

Attributions: EBI_InterProScan_tmhmm_signalp EBI_Phobius tmap_single_sequence

License: Creative Commons Attribution 3.0 Unported License

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. Transmembrane and signal...