Workflows

EBI_InterProScan_with_prompts (1)

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Note: the WSInterProScan web service used by this workflow is no longer available haveing been replaced by the EMBL-EBI's InterProScan (REST) (http://www.ebi.ac.uk/Tools/webservices/services/pfa/iprscan_rest) and InterProScan (SOAP) (http://www.ebi.ac.uk/Tools/webservices/services/pfa/iprscan_soap) web services. Thus the workflow described here no longer works, see the alternative workflows for the InterProScan (SOAP) service for workflows which use the new services. Run an InterProScan anal...

Created: 2008-05-31 | Last updated: 2011-04-01

Credits: Hamish McWilliam

Attributions: EBI_InterProScan

EBI InterproScan T2 (1)

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This T2 version of the Interpro scan workflow is an example of the while loop in action. This is used to poll the async EBI service for the result (busy waiting)

Created: 2009-06-30 | Last updated: 2009-06-30

Credits: Stian Soiland-Reyes Katy Wolstencroft

Attributions:

EBI_TCoffee (1)

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Perform a multiple sequence alignment using T-Coffee (see http://www.tcoffee.org/). The EBI's WSTCoffee web service (see http://www.ebi.ac.uk/Tools/webservices/services/tcoffee) is used. Note: the WSTCoffee 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 T-COFFEE services (REST or SOAP) should be used instead.  

Created: 2008-06-03 | Last updated: 2010-12-06

Credits: Hamish McWilliam

EBI_MUSCLE (1)

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Perform a multiple sequence alignment using the MUSCLE tool (see http://www.drive5.com/muscle/). The EBI's WSMuscle web service (see http://www.ebi.ac.uk/Tools/webservices/services/muscle) is used. Note: the WSMuscle 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 MUSCLE services (REST or SOAP) should be used instead.  

Created: 2008-06-03 | Last updated: 2010-12-06

Credits: Hamish McWilliam

workflow1 (1)

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blast dando o ID de uma proteinablast dando o ID de uma proteina ex: database is ‘SWISS’, for program, ‘blastp’, and for ID ‘1220173blast dando o ID de uma proteina with interpro scan ex: database is SWISS’, for program, blastp, and for ID 1220173blast dando o ID de uma proteina ex: database is SWISS’, for program, blastp, and for ID 1220173

Created: 2009-11-16

Credits: Jorgep

Attributions: EBI_InterProScan for Taverna 2

Ex (1)

Ex of exercise

Created: 2009-11-16

Credits: Mventosa

Attributions: EBI_InterProScan for Taverna 2

EBI_MAFFT (1)

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Perform a multiple sequence alignment using the MAFFT tool (see http://align.bmr.kyushu-u.ac.jp/mafft/software/). The EBI's WSMafft web service (see http://www.ebi.ac.uk/Tools/webservices/services/mafft) is used to access to tool. Note: the WSMafft 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 MAFFT services (REST or SOAP) should be used instead.

Created: 2008-06-03 | Last updated: 2010-12-06

Credits: Hamish McWilliam

EBI_MPsrch (1)

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Run a Smith-Waterman sequence search using the EBI’s WSMPsrch service (see http://www.ebi.ac.uk/Tools/webservices/services/mpsrch). Note: the WSMPsrch service used by this workflow was retired 27th January 2010. Equivalent functionality is available in the EBI's FASTA (REST or SOAP) and PSI-Search (REST or SOAP) services.  

Created: 2008-06-02 | Last updated: 2010-12-06

Credits: Hamish McWilliam

EBI_Kalign (1)

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Multiple sequence alignment using the Kalign tool. This workflow uses the EBI's WSKalign service (see http://www.ebi.ac.uk/Tools/webservices/services/kalign) to access the Kalign tool. The set of sequences to align and the molecule type (protein or nucleic acid) are the input, the other parameters for the search (see Job_params) are allowed to default. Note: the WSKalign service used by this workflow is deprecated as of 21st September 2010 and should not be used in any new development. Thi...

Created: 2008-06-02 | Last updated: 2010-12-06

Credits: Hamish McWilliam

EBI_blastpgp_PSI-BLAST (1)

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Perform a PSI-BLAST iterative search using the EBI’s WSBlastpgp service (see http://www.ebi.ac.uk/Tools/webservices/services/blastpgp). The query sequence, database to search and users e-mail address are inputs, the other parameters for the search (see Job_params) are allowed to default. In most cases you will probably want to adjust the expectation thresholds and the maximum number of iterations for your specific query sequence and the database being searched.

Created: 2008-05-31

Credits: Hamish McWilliam