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Tag: ebi
Original Uploader

Workflow EBI_InterProScan (3)

Created: 26/10/08 @ 20:33:34 | Last updated: 01/04/11 @ 08:52:28

Credits: User Hamish McWilliam

License: Creative Commons Attribution 3.0 Unported License

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Note: the WSInterProScan web service used by this workflow is no longer available haveing been replaced by the EMBL-EBI's InterProScan (REST) (http://www.ebi.ac.uk/Tools/webservices/services/pfa/iprscan_rest) and InterProScan (SOAP)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. Perform an InterProScan ...

Rating: 0.0 / 5 (0 ratings) | Versions: 3 | Reviews: 0 | Comments: 1 | Citations: 0

Viewed: 1444 times | Downloaded: 401 times

Tags (10):

Original Uploader

Workflow Nucleotide_InterProScan (4)

Created: 26/10/08 @ 21:10:09 | Last updated: 01/04/11 @ 08:54:21

Credits: User Hamish McWilliam

Attributions: Workflow EBI_InterProScan Workflow EBI_NCBI_BLAST Workflow Nucleotide_ORF_translation Workflow Fasta_string_to_fasta_list Workflow Sequence_or_ID

License: Creative Commons Attribution 3.0 Unported License

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Note: the WSInterProScan web service used by this workflow is no longer available haveing been replaced by the EMBL-EBI's InterProScan (REST) (http://www.ebi.ac.uk/Tools/webservices/services/pfa/iprscan_rest) and InterProScan (SOAP)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 InterProScan using a...

Rating: 0.0 / 5 (0 ratings) | Versions: 4 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 415 times | Downloaded: 125 times

Tags (11):

Original Uploader

Workflow EBI_Blast2InterPro (2)

Created: 26/10/08 @ 20:45:45 | Last updated: 22/08/12 @ 11:22:43

Credits: User Hamish McWilliam

Attributions: Workflow EBI_WU-BLAST Workflow EBI_dbfetch_fetchBatch Workflow Fasta_string_to_fasta_list Workflow EBI_InterProScan

License: Creative Commons Attribution 3.0 Unported License

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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. Perform a BLAST search a...

Rating: 5.0 / 5 (1 rating) | Versions: 2 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 272 times | Downloaded: 103 times

Tags (11):

Original Uploader

Workflow EBI_ClustalW2 (2)

Created: 07/04/09 @ 20:06:03 | Last updated: 06/12/10 @ 11:00:19

Credits: User Hamish McWilliam

License: Creative Commons Attribution 3.0 Unported License

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Perform a ClustalW multiple sequence alignment using the EBI’s WSClustalW2 service (see http://www.ebi.ac.uk/Tools/webservices/services/clustalw2). The set of sequences to align are the input, the other parameters for the search (see Job_params) are allowed to default. Note: the WSClustalW2 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 ClustalW2 servi...

Rating: 0.0 / 5 (0 ratings) | Versions: 2 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 563 times | Downloaded: 250 times

Tags (7):

Original Uploader

Workflow Protein_search_fetch_align_tree (2)

Created: 07/04/09 @ 20:13:19

Credits: User Hamish McWilliam

Attributions: Workflow EBI_ClustalW2 Workflow EBI_ClustalW2_phylogentic_tree Workflow EBI_dbfetch_fetchBatch Workflow EBI_WU-BLAST

License: Creative Commons Attribution 3.0 Unported License

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An implmentation of the classical sequence analysis workflow: Find homologues (sequence similarity search) Fetch homologues Align homologues (multiple sequence alignment) Produce phylogenetic tree In this implementation the EBI webservices are used: WU-BLAST (WSWUBlast) blastp vs. UniProtKB dbfetch (WSDbfetch) ClustalW (WSClustalW2) ClustalW (WSClustalW2) Note: this version does not add the inital query sequence to the alignment, and so is most useful when used with the identifers...

Rating: 0.0 / 5 (0 ratings) | Versions: 2 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 463 times | Downloaded: 154 times

Tags (15):

Original Uploader

Workflow Protein_transmembrane_prediction (2)

Created: 26/10/08 @ 21:16:10 | Last updated: 01/04/11 @ 08:57:10

Credits: User Hamish McWilliam

Attributions: Workflow EBI_InterProScan_tmhmm_signalp Workflow EBI_Phobius Workflow tmap_single_sequence

License: Creative Commons Attribution 3.0 Unported License

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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. Transmembrane and signal...

Rating: 4.5 / 5 (2 ratings) | Versions: 2 | Reviews: 0 | Comments: 3 | Citations: 0

Viewed: 406 times | Downloaded: 92 times

Tags (11):

Original Uploader

Workflow EBI_InterProScan_tmhmm_signalp (4)

Created: 26/10/08 @ 20:50:10 | Last updated: 01/04/11 @ 08:56:37

Credits: User Hamish McWilliam

Attributions: Workflow EBI_InterProScan

License: Creative Commons Attribution 3.0 Unported License

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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. Use the TMHMM and Signal...

Rating: 0.0 / 5 (0 ratings) | Versions: 4 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 219 times | Downloaded: 89 times

Tags (8):

Original Uploader

Workflow EBI_PICR_Sequence_to_UniParc_and_InterPro (2)

Created: 08/06/08 @ 13:53:39 | Last updated: 08/06/08 @ 14:10:02

Credits: User Hamish McWilliam

Attributions: Workflow EBI_dbfetch_UniParc Workflow EBI_Fetch_InterPro_Matches_UniParc Workflow EBI_PICR_Sequence_to_ID

License: Creative Commons Attribution 3.0 Unported License

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Given a protein sequence get some information about it: Does this protein sequence occur in any of the protein databases (e.g. UniProtKB, PDB, etc.). Using the PICR web service (see http://www.ebi.ac.uk/Tools/picr/) map the sequence to a UniParc identifer. Which entries in the protein databases have this sequence. Using the UniParc database (see http://www.ebi.ac.uk/uniprot/database/DBDescription.html#uniparc) a summary of the databases and the entries in those databases which have this s...

Rating: 4.0 / 5 (1 rating) | Versions: 2 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 170 times | Downloaded: 60 times

Tags (13):

Original Uploader

Workflow EBI_NCBI_BLAST (1)

Created: 31/05/08 @ 08:38:46 | Last updated: 06/12/10 @ 10:54:16

Credits: User Hamish McWilliam

License: Creative Commons Attribution 3.0 Unported License

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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...

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

Viewed: 348 times | Downloaded: 166 times

Tags (6):

Original Uploader

Workflow EBI WU-BLAST with program and database sel... (3)

Created: 04/07/09 @ 11:39:54 | Last updated: 06/12/10 @ 10:56:44

Credits: User Hamish McWilliam

Attributions: Workflow EBI_WU-BLAST

License: Creative Commons Attribution 3.0 Unported License

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Run a BLAST analysis using the EBI's WSWUBlast service (see http://www.ebi.ac.uk/Tools/webservices/services/wublast). This workflow wraps the EBI_WU-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. The values presented in the selection menus for the program and database are obtained from the service, using the provided me...

Rating: 0.0 / 5 (0 ratings) | Versions: 3 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 207 times | Downloaded: 86 times

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