EBI NCBI BLAST Multi FASTA

Created: 2011-07-16 19:08:38 Last updated: 2011-07-16 19:35:11

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This workflow performs multiple sequence similarity searches using the NCBI blast at the EBI. It uses the new EBI services, which are asynchronous and require looping over the nested workflow (Status) until the workflow has finished. Many of the EBI services now work in this way, so you can use this workflow as an example of the invocation pattern and looping configuration.

If you want to make a blast search for more than 10 sequences I would recommend you to run the workflow using the command line. For instance: executeworkflow.bat -embedded -inputvalue email your@email.com -inputfile yourfile.txt EBI_NCBI_BLAST-multifasta.t2flow

More docuemtnation about how to use the command line tool in http://www.taverna.org.uk/documentation/taverna-2-x/command-line-tool/2-3/

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Workflow Components

Authors (1)

Titles (1)

Descriptions (1)

Dependencies (0)

Inputs (2)

Name	Description
multiFasta
email

Processors (2)

Name	Type	Description
EBI_NCBI_BLAST	workflow
Fasta_string_to_fasta_list	workflow

Beanshells (1)

Name	Description	Inputs	Outputs
Add_angle		stripped_fasta	full_fasta

Outputs (4)

Name	Description
output
output_status
graphic_output
original_output

Datalinks (7)

Source	Sink
Fasta_string_to_fasta_list:fasta_list	EBI_NCBI_BLAST:sequence
email	EBI_NCBI_BLAST:email
multiFasta	Fasta_string_to_fasta_list:fasta_string
EBI_NCBI_BLAST:getResult_2_output_output	output
EBI_NCBI_BLAST:getStatus_output_status	output_status
EBI_NCBI_BLAST:getResult_graphic_output_output	graphic_output
EBI_NCBI_BLAST:getResult_original_output	original_output

Coordinations (0)

Information Workflow Type

Taverna 2

Information Uploader

Rafael C. Jimenez

Information License

All versions of this Workflow are licensed under:

Information Version 1 (earliest) (of 2)

Information Credits (1)

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Rafael C. Jimenez

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None

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Information Statistics

2540 viewings

1591 downloads

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Citations (0)

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Version History

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EBI NCBI BLAST Multi FASTA

Created by Rafael C. Jimenez on Saturday 16 July 2011 19:08:38 (UTC)
EBI NCBI BLAST Multi FASTA

Created by Rafael C. Jimenez on Saturday 16 July 2011 19:35:10 (UTC)

Revision comment:

Some input examples added.

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Attributions: EBI_NCBI_BLAST NCBI BLAST (SOAP)

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Credits: Hamish McWilliam

Attributions: EBI_NCBI_BLAST NCBI BLAST (SOAP)