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NCBI BLAST (SOAP)

Workflow Entry: NCBI BLAST (SOAP)

Created at: 29/11/10 @ 20:46:58 Last updated: 28/03/13 @ 12:45:26

Version 1 (of 1)

Version created on: 29/11/10 @ 20:46:58 by: Hamish McWilliam

Title: NCBI BLAST (SOAP)

Type: Taverna 1

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Description

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 See the Service entry for this web service.
parametersXML	local
parametersXML1	local
parametersXML2	local
getResult	arbitrarywsdl	Get a job result formatted using a particular renderer See the Service entry for this web service.
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 Original Uploader

Hamish McWilliam

Information License

All versions of this Workflow are licensed under:

Apache License v2.0

Information Credits (1)

(People/Groups)

Hamish McWilliam

Information Attributions (2)

(Workflows/Files)

Information Tags (7)

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Information Shared with Groups (0)

None

Information Featured In Packs (1)

EMBL-EBI Web Services

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Information Ratings (0)

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Information Attributed By (1)

(Workflows/Files)

NCBI BLAST (SOAP)

Information Favourited By (0)

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Information Statistics

171 viewings

447 downloads

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Citations (0)

None

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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NCBI BLAST (SOAP) (1)

Created: 29/11/10 @ 20:03:13 | Last updated: 28/03/13 @ 12:44:56

Attributions: EBI_NCBI_BLAST NCBI BLAST (SOAP)

License: Apache License v2.0

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 74 times | Downloaded: 102 times

Tags (7):

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Blast Report from ID (1)

Created: 07/04/11 @ 22:28:28 | Last updated: 07/04/11 @ 22:39:44

Credits: Hectorj2f

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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...