NCBI BLAST (SOAP)

Created: 2010-11-29 20:46:58 Last updated: 2013-03-28 12:45:26

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Perform a BLAST search using the EMBL-EBIâ€™s NCBI BLAST (SOAP) service (see http://www.ebi.ac.uk/Tools/webservices/services/sss/ncbi_blast_soap). The query sequence, database to search and BLAST program to use are inputs, the other parameters for the search are allowed to default.

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Workflow Components

Inputs (5)

Name	Description
Email	Your e-mail address. For example: email@example.org.
Program	NCBI BLAST program to use for search. For example: blastp.
Databases	List of databases to search. For example: uniprotkb_swissprot.
Sequence	Query sequence. Either sequence data in any common format, or an entry identifier in DB:ID format. For example: uniprot:wap_rat.
Sequence_type	Query sequence type. Either protein or nucleotide.

Processors (9)

Name	Type	Description
run	arbitrarywsdl	Submit an analysis job
parametersXML	local
parametersXML1	local
parametersXML2	local
getResult	arbitrarywsdl	Get a job result formatted using a particular renderer
parametersXML3	local
parametersXML4	local
Job_status_poll	workflow
Byte___to_String	local

Beanshells (1)

Name	Description	Inputs	Outputs
Is_Running		job_status	is_running

Outputs (3)

Name	Description
JobId
Job_status
Result

Links (16)

Source	Sink
Databases	parametersXML1:database
Email	parametersXML:email
Program	parametersXML1:program
Sequence	parametersXML1:sequence
Sequence_type	parametersXML1:stype
Byte___to_String:string	Result
Job_status_poll:Job_Status	Job_status
getResult:parameters	parametersXML4:input
parametersXML1:output	parametersXML:parameters
parametersXML2:jobId	Job_status_poll:JobId
parametersXML2:jobId	parametersXML3:jobId
parametersXML3:output	getResult:parameters
parametersXML4:output	Byte___to_String:bytes
parametersXML2:jobId	JobId
parametersXML:output	run:parameters
run:parameters	parametersXML2:input

Coordinations (1)

Controller	Target
Job_status_poll	getResult

Information Workflow Type

Taverna 1

Information Uploader

Hamish McWilliam

Information License

All versions of this Workflow are licensed under:

Apache License v2.0

Information Version 1 (of 1)

Information Credits (1)

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Hamish McWilliam

Information Attributions (2)

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Information Tags (7)

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Information Featured In Packs (1)

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Information Attributed By (1)

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NCBI BLAST (SOAP)

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Information Statistics

2431 viewings

1795 downloads

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Version History

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NCBI BLAST (SOAP)

Created by Hamish McWilliam on Monday 29 November 2010 20:46:58 (UTC)

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Created: 2010-11-29 | Last updated: 2013-03-28

Attributions: EBI_NCBI_BLAST NCBI BLAST (SOAP)

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This workflow retrieves a fasta sequence or blast report from an id. Firstly, given some inputs (e.g. ids:EDL10223.1, format:fasta, style:default and db:emblcds), it returns the sequence in fasta format associated to those inputs using the EBI's WSDbfetch web service (see http://www.ebi.ac.uk/Tools/webservices/services/dbfetch). Next, we obtain a Blast report from this fasta sequence and some others parameters. The final result in that case corresponds with the same fasta sequence introduced...

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Credits: Hectorj2f