EBI FASTA with prompts

Created: 2008-05-30 23:53:16 Last updated: 2010-12-06 10:53:23

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Run a FASTA analysis using the EBIâ€™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.

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Workflow Components

Inputs (0)

Processors (7)

Name	Type	Description
Make_database_list	local	List of available databases.
Make_FASTA_program_list	local	List of available FASTA programs.
Ask_for_sequence	local	Ask for the query sequence, either as a sequence identifier in database:identifer format (e.g. uniprot:wap_rat) or the actual sequence (fasta format recommended).
Ask_for_email	local	Ask for the user's e-mail address.
Select_database	local	Select the required database.
Select_FASTA_program	local	Select the required FASTA program.
EBI_FASTA	workflow	Run a FASTA or SSEARCH job.

Beanshells (0)

Outputs (1)

Name	Description
FASTA_report	Plain text FASTA report.

Links (7)

Source	Sink
Ask_for_email:answer	EBI_FASTA:E-mail
Ask_for_sequence:answer	EBI_FASTA:Sequence_or_ID
EBI_FASTA:FASTA_Text_Result	FASTA_report
Make_FASTA_program_list:split	Select_FASTA_program:valueList
Make_database_list:split	Select_database:valueList
Select_FASTA_program:answer	EBI_FASTA:FASTA_Program
Select_database:answer	EBI_FASTA:Database

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Information Workflow Type

Taverna 1

Information Uploader

Hamish McWilliam

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Information Version 2 (of 3)

Information Credits (1)

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Hamish McWilliam

Information Attributions (1)

(Workflows/Files)

EBI_FASTA

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Information Statistics

4146 viewings

3086 downloads

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Version History

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EBI FASTA with prompts

Created by Hamish McWilliam on Friday 30 May 2008 23:53:16 (UTC)
EBI FASTA with prompts

Created by Hamish McWilliam on Friday 30 May 2008 23:53:16 (UTC)

Last edited by Hamish McWilliam on Saturday 31 May 2008 00:14:20 (UTC)

Revision comment:

Fix disappearing nested workflow.
EBI FASTA with prompts

Created by Hamish McWilliam on Friday 30 May 2008 23:53:16 (UTC)

Last edited by Hamish McWilliam on Monday 06 December 2010 10:53:23 (UTC)

Revision comment:

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Taverna 1

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Hamish McWilliam

EBI_FASTA (1)

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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.

Created: 2008-05-30 | Last updated: 2010-12-06

Credits: Hamish McWilliam

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Protein_alignment_transmembrane (1)

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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...

Created: 2008-06-01

Credits: Hamish McWilliam

Attributions: EBI_FASTA EBI_ClustalW2 EBI_dbfetch_fetchBatch