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EBI_ClustalW2

Workflow Entry: EBI_ClustalW2

Created at: 07/04/09 @ 20:06:03 Last updated: 06/12/10 @ 11:00:19

Version 2 (latest) (of 2)

Version created on: 07/04/09 @ 20:06:03 by: Hamish McWilliam | Revision comments Expand

Last edited on: 06/12/10 @ 11:00:19 by: Hamish McWilliam

Title: EBI_ClustalW2

Type: Taverna 1

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Description

Perform a ClustalW multiple sequence alignment using the EBI’s WSClustalW2 service (see http://www.ebi.ac.uk/Tools/webservices/services/clustalw2). The set of sequences to align are the input, the other parameters for the search (see Job_params) are allowed to default.

Note: the WSClustalW2 service used by this workflow is deprecated as of 21st September 2010 and should not be used in any new development. This service is will be retired during 2011. EBI's replacement ClustalW2 services (REST or SOAP) should be used instead.

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Workflow Components

Inputs (2)

Name	Description
Sequences	Sequences to align (fasta format recommended).
Email_address	User e-mail address.

Processors (11)

Name	Type	Description
runClustalW2	arbitrarywsdl	Submit a ClustalW analysis job (see http://www.ebi.ac.uk/Tools/webservices/services/clustalw2#runclustalw2_params_content) See the Service entry for this web service.
Job_params	local
Content_list	local
Input_data	local
Get_alignment_result	arbitrarywsdl	Get the results of a job (see http://www.ebi.ac.uk/Tools/webservices/services/clustalw2#poll_jobid_type) See the Service entry for this web service.
Get_guide_tree_result	arbitrarywsdl	Get the results of a job (see http://www.ebi.ac.uk/Tools/webservices/services/clustalw2#poll_jobid_type) See the Service entry for this web service.
Unpack_alignment_result	local
Unpack_guide_tree_result	local
EBI_ClustalW2_poll_job	workflow	Check for job status, and wait if job not finished.
Get_output_result	arbitrarywsdl	Get the results of a job (see http://www.ebi.ac.uk/Tools/webservices/services/clustalw2#poll_jobid_type) See the Service entry for this web service.
Unpack_output_result	local

Beanshells (1)

Name	Description	Inputs	Outputs
Is_done	Map job status into true/false is done flag	job_status	is_done

Outputs (4)

Name	Description
ClustalW_alignment	The alignment in ClustalW format.
ClustalW_guide_tree	Guide tree used to produce the final alignment.
Job_ID	EBI job identifier
ClustalW_output

Links (16)

Source	Sink
Email_address	Job_params:email
Content_list:output	runClustalW2:content
Get_alignment_result:result	Unpack_alignment_result:bytes
Get_guide_tree_result:result	Unpack_guide_tree_result:bytes
Get_output_result:result	Unpack_output_result:bytes
Input_data:output	Content_list:WSArrayofData
Job_params:output	runClustalW2:params
Sequences	Input_data:content
Unpack_alignment_result:string	ClustalW_alignment
Unpack_guide_tree_result:string	ClustalW_guide_tree
Unpack_output_result:string	ClustalW_output
runClustalW2:jobid	EBI_ClustalW2_poll_job:Job_ID
runClustalW2:jobid	Get_alignment_result:jobid
runClustalW2:jobid	Get_guide_tree_result:jobid
runClustalW2:jobid	Get_output_result:jobid
runClustalW2:jobid	Job_ID

Coordinations (3)

Controller	Target
EBI_ClustalW2_poll_job	Get_alignment_result
EBI_ClustalW2_poll_job	Get_guide_tree_result
EBI_ClustalW2_poll_job	Get_output_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)

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None

Information Tags (7)

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Information Shared with Groups (0)

None

Information Featured In Packs (2)

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EBI Web Services

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Information Attributed By (5)

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Information Favourited By (0)

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Information Statistics

2980 viewings

1553 downloads

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Citations (0)

None

Version History

Earliest Version:
[1] - EBI_ClustalW2

Created on: Saturday 31 May 2008 @ 10:27:58 (GMT)

Created by: Hamish McWilliam

Last edited on: Monday 02 June 2008 @ 21:27:39 (GMT)

Last edited by: Hamish McWilliam

Revision comments:

None

Latest Version:
[2] - EBI_ClustalW2

Created on: Tuesday 07 April 2009 @ 20:06:03 (GMT)

Created by: Hamish McWilliam

Last edited on: Monday 06 December 2010 @ 11:00:19 (GMT)

Last edited by: Hamish McWilliam

Revision comments:

Update for changes in nomenclature used in web service.

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Other workflows that use similar services (7)

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

Taverna 1

Original Uploader

Hamish McWilliam

Protein_search_fetch_align_tree (v2)

Created: 07/04/09 @ 20:13:19

Credits: Hamish McWilliam

Attributions: EBI_ClustalW2 EBI_ClustalW2_phylogentic_tree EBI_dbfetch_fetchBatch EBI_WU-BLAST

License: Creative Commons Attribution 3.0 Unported License

An implmentation of the classical sequence analysis workflow: Find homologues (sequence similarity search) Fetch homologues Align homologues (multiple sequence alignment) Produce phylogenetic tree In this implementation the EBI webservices are used: WU-BLAST (WSWUBlast) blastp vs. UniProtKB dbfetch (WSDbfetch) ClustalW (WSClustalW2) ClustalW (WSClustalW2) Note: this version does not add the inital query sequence to the alignment, and so is most useful when used with the identifers...

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

Viewed: 403 times | Downloaded: 133 times

Tags (15):

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Taverna 2

Original Uploader

Achille Zappa

Workflow for Automated Comparative Protein Sequences Analysis (v2)

Created: 29/06/10 @ 12:59:57 | Last updated: 31/08/10 @ 09:43:41

Credits: Achille Zappa

Attributions: EBI_ClustalW_alignment_tree

License: Creative Commons Attribution-No Derivative Works 3.0 Unported License

This workflow performs "parallel" generic protein sequence analysis. In order to do that a list of known protein identifiers chosen by the biologist enters into the software to perform different multiple sequence alignments and finally phylogenetic analysis.

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

Viewed: 44 times | Downloaded: 10 times

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Linked Data

Non-Information Resource URI: http://www.myexperiment.org/workflows/203

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