EBI NCBI Blast

Created: 2007-10-03 18:36:22

Download Workflow

EBI NCBI Blast

Preview

Run

Run this Workflow in the Taverna Workbench...

Option 1:

Copy and paste this link into File > 'Open workflow location...'
http://www.myexperiment.org/workflows/39/download?version=2
[ More Info Expand ]

Workflow Components

Inputs (1)

Name	Description
sequence

Processors (7)

Name	Type	Description
contentXML	local
paramsXML	local
WSArrayofDataXML	local
runNCBIBlast	arbitrarywsdl
poll	arbitrarywsdl
Nested_Workflow1	workflow
Byte___to_String	local

Beanshells (0)

Outputs (2)

Name	Description
result
jobid

Links (9)

Source	Sink
WSArrayofDataXML:output	contentXML:WSArrayofData
contentXML:output	runNCBIBlast:content
paramsXML:output	runNCBIBlast:params
sequence	WSArrayofDataXML:content
Byte___to_String:string	result
poll:output	Byte___to_String:bytes
runNCBIBlast:jobid	Nested_Workflow1:job
runNCBIBlast:jobid	poll:jobid
runNCBIBlast:jobid	jobid

Coordinations (1)

Controller	Target
Nested_Workflow1	poll

Information Workflow Type

Taverna 1

Information Uploader

Hong Chang Bum

Information License

All versions of this Workflow are licensed under:

Information Version 2 (latest) (of 2)

Information Credits (0)

(People/Groups)

None

Information Attributions (0)

(Workflows/Files)

None

Information Tags (3)

Uploader tags

Log in to add Tags

Information Shared with Groups (0)

None

Information Featured In Packs (0)

None

Log in to add to one of your Packs

Information Attributed By (0)

(Workflows/Files)

None

Information Favourited By (2)

Information Statistics

3938 viewings

3138 downloads

[ see breakdown ]

Citations (0)

None

Version History

In chronological order:

ebi_ncbi

Created by Hong Chang Bum on Wednesday 03 October 2007 18:36:22 (UTC)
EBI NCBI Blast

Created by Hong Chang Bum on Wednesday 03 October 2007 18:36:22 (UTC)

Reviews (0)

No reviews yet

Be the first to review!

Comments (3)

View Timeline

Log in to make a comment

Gescl

Workflow as it is now does not work.

"Sequence" should only be linked to the "content" input parameter of WSArrayofDataXML splitter and not to the "database" input parameter of the paramsXML splitter.

At least 3 extra parameters need to be created: "database" and "program" linked to corresponding parameters of paramsXML and "type" linked to the corresponding input parameter of WSArrayofDataXML.

Franck Tanoh

Test the workflow with the following parameter it should work. it only does a blastp.

input example:

>gi|37927048|pdb|1NYC|A Chain A, Staphostatins Resemble Lipocalins, Not Cystatins In Fold.

GSMYQLQFINLVYDTTKLTHLEQTNINLFIGNWSNHQLQKSICIRHGDDTSHNQYHILFIDTAHQRIKFS

SFDNEEIIYILDYDDTQHILMQTSSKQGIGTSRPIVYERLV

Liyinji	Tuesday 24 August 2010 17:53:46 (UTC)
	aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa

Other workflows that use similar services (3)

Only the first 2 workflows that use similar services are shown. View all workflows that use these services.

Taverna 1

Uploader

Hamish McWilliam

EBI_NCBI_BLAST (1)

Download

Perform a BLAST search using the EBI’s WSNCBIBlast service (see http://www.ebi.ac.uk/Tools/webservices/services/ncbiblast). The query sequence, database to search and BLAST program to use are inputs, the other parameters for the search (see Job_params) are allowed to default. Note: the WSNCBIBlast 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 NCBI BLA...

Created: 2008-05-31 | Last updated: 2010-12-06

Credits: Hamish McWilliam

Taverna 1

Uploader

Hamish McWilliam

EBI_NCBI_BLAST_with_prompts (1)

Download

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

Created: 2008-05-31 | Last updated: 2010-12-06

Credits: Hamish McWilliam

Attributions: EBI_NCBI_BLAST