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EBI_FASTA

Workflow Entry: EBI_FASTA

Created at: 30/05/08 @ 23:50:46 Last updated: 06/12/10 @ 10:52:25

Version 1 (of 1)

Version created on: 30/05/08 @ 23:50:46 by: Hamish McWilliam

Last edited on: 06/12/10 @ 10:52:25 by: Hamish McWilliam

Title: EBI_FASTA

Type: Taverna 1

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Description

Run a FASTA or SSEARCH sequence similarity search using the EBI's WSFasta service (see http://www.ebi.ac.uk/Tools/webservices/services/fasta).

Note: the WSFasta 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 FASTA services (REST or SOAP) should be used instead.

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http://www.myexperiment.org/workflows/199/download?version=1
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Workflow Components

Inputs (4)

Name	Description
Sequence_or_ID	Query sequence (fasta format recommended) or sequence identifer in database:identifer format (e.g. uniprot:wap_rat).
Database	The database to search (e.g. uniprot).
E-mail	Your e-mail address.
FASTA_Program	The FASTA program to run (e.g. fasta3, fastf3, fasts3, fastx3, fasty3, tfastx, tfasty).

Processors (10)

Name	Type	Description
runFasta	arbitrarywsdl	Submit the FASTA/SSEARCH job. See the Service entry for this web service.
Poll_FASTA_Job	workflow	Check for job completion.
Input_data_list	local	Wrap the input sequence in a list.
Input_data	local	Input data structure, adds a type to the input sequence.
FASTA_job_params	local	Parameters for the FASTA/SSEARCH job.
getIds	arbitrarywsdl	Get the hit identifers. See the Service entry for this web service.
Get_Text_Result	arbitrarywsdl	Get the FASTA report as text. See the Service entry for this web service.
Get_XML_Result	arbitrarywsdl	Get the FASTA report as XML. See the Service entry for this web service.
Unpack_Text_Result	local	Unpack plain text FASTA report from byte[] into string.
Unpack_XML_Result	local	Unpack XML FASTA report from byte[] into string.

Beanshells (1)

Name	Description	Inputs	Outputs
Is_Done		job_status	is_done

Outputs (4)

Name	Description
FASTA_Text_Result	FASTA program output as plain text. Note the exact format of the output depends on the chosen FASTA program.
FASTA_XML_Result	FASTA output in an XML format.
Hit_ID_List	List of the identifiers of the hits found.
Job_ID	The identifier of the job at EBI.

Links (17)

Source	Sink
Database	FASTA_job_params:database
E-mail	FASTA_job_params:email
FASTA_Program	FASTA_job_params:program
Get_Text_Result:output	Unpack_Text_Result:bytes
Get_XML_Result:output	Unpack_XML_Result:bytes
Input_data:output	Input_data_list:WSArrayofData
Input_data_list:output	runFasta:content
Sequence_or_ID	Input_data:content
FASTA_job_params:output	runFasta:params
Unpack_Text_Result:string	FASTA_Text_Result
Unpack_XML_Result:string	FASTA_XML_Result
runFasta:jobid	Get_Text_Result:jobid
runFasta:jobid	Get_XML_Result:jobid
getIds:result	Hit_ID_List
runFasta:jobid	getIds:jobid
runFasta:jobid	Job_ID
runFasta:jobid	Poll_FASTA_Job:Job_ID

Coordinations (3)

Controller	Target
Poll_FASTA_Job	getIds
Poll_FASTA_Job	Get_Text_Result
Poll_FASTA_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)

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Hamish McWilliam

Information Attributions (0)

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Information Tags (6)

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Information Featured In Packs (2)

Private pack
EMBL-EBI Web Services (retired)

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Information Attributed By (2)

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Information Statistics

1063 viewings

1007 downloads

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Citations (0)

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Version History

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EBI_FASTA

Created by Hamish McWilliam on Friday 30 May 2008 @ 23:50:46 (UTC)

Last edited by Hamish McWilliam on Monday 06 December 2010 @ 10:52:25 (UTC)

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Other workflows that use similar services (2)

Taverna 1

Original Uploader

Hamish McWilliam

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EBI FASTA with prompts (3)

Created: 30/05/08 @ 23:53:16 | Last updated: 06/12/10 @ 10:53:23

Credits: Hamish McWilliam

Attributions: EBI_FASTA

License: Creative Commons Attribution 3.0 Unported License

Run a FASTA analysis using the EBI’s WSFasta service (see http://www.ebi.ac.uk/Tools/webservices/services/fasta). This workflow wraps the EBI_FASTA workflow to provide a basic user interface which prompts for the required inputs: sequence, database, FASTA program and user e-mail. Other parameters (e.g. matrix, gap penalties, etc.) are allowed to default. Note: the WSFasta service used by this workflow is deprecated as of 21st September 2010 and should not be used in any new developme...

Rating: 0.0 / 5 (0 ratings) | Versions: 3 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 119 times | Downloaded: 58 times

Tags (7):

Taverna 1

Original Uploader

Hamish McWilliam

View

Download (v1)

Protein_alignment_transmembrane (1)

Created: 01/06/08 @ 12:20:29

Credits: Hamish McWilliam

Attributions: EBI_FASTA EBI_ClustalW2 EBI_dbfetch_fetchBatch

License: Creative Commons Attribution 3.0 Unported License

Transmembrane domain prediction using EMBOSS tmap with an input sequence alignment of homolouges: Sequence similarity search (SSS) to find homologues Fetch sequences of hits Multiple sequence alignment (MSA) of hit sequences EMBOSS tmap with alignment from 3. Uses the EBI web services: WSFasta (see http://www.ebi.ac.uk/Tools/webservices/services/fasta) WSDbfetch (see http://www.ebi.ac.uk/Tools/webservices/services/dbfetch) WSClustalW2 (see http://www.ebi.ac.uk/Tools/webservices/servic...