Workflow Entry: EBI_Phobius

Created at: 01/06/08 @ 11:08:46 Last updated: 02/06/08 @ 21:39:07

Version 2 (latest) (of 2)

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

Launch in Taverna

Note: you need to have both the WHIP Launcher and the Taverna myExperiment/WHIP plugin installed on your machine for this to work. See here for information.

Option 2:

Copy and paste this link into File > 'Open workflow location...'
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)
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)
EBI_Phobius_poll_job	workflow	Check for job completion.
Format_as_GFF	beanshell

Outputs (3)

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

Links (12)

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