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Items tagged with "interpro" (13)

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Workflows (13)
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Note: the WSInterProScan web service used by this workflow is no longer available haveing been replaced by the EMBL-EBI's InterProScan (REST) (http://www.ebi.ac.uk/Tools/webservices/services/pfa/iprscan_rest) and InterProScan (SOAP)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 EBI_InterProScan_with_prompts (1)

Created: 31/05/08 @ 11:40:34 | Last updated: 01/04/11 @ 08:57:45

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Note: the WSInterProScan web service used by this workflow is no longer available haveing been replaced by the EMBL-EBI's InterProScan (REST) (http://www.ebi.ac.uk/Tools/webservices/services/pfa/iprscan_rest) and InterProScan (SOAP)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

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

Viewed: 88 times | Downloaded: 51 times

Tags (7):

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_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_Fetch_InterPro_Matches_UniParc (1)

Created: 08/06/08 @ 14:08:47

Credits: User Hamish McWilliam

License: Creative Commons Attribution 3.0 Unported License

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For a UniParc (see http://www.ebi.ac.uk/uniprot/database/DBDescription.html#uniparc) identifier/accession fetch the assocated InterPro Matches from SRS@EBI (see http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-page+LibInfo+-lib+IPRMC_UNIPARC).

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

Viewed: 74 times | Downloaded: 35 times

Tags (9):

Original Uploader

Workflow EBI_InterProScan for Taverna 2 (2)

Created: 26/01/10 @ 14:46:07 | Last updated: 26/01/10 @ 14:46:08

Credits: User Stian Soiland-Reyes User Paolo User Katy Wolstencroft User Hamish McWilliam

Attributions: Workflow EBI InterproScan T2 Workflow EBI_InterProScan

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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Perform an InterProScan analysis of a protein sequence using the EBI’s WSInterProScan service (see http://www.ebi.ac.uk/Tools/webservices/services/interproscan). The input sequence to use and the user e-mail address are inputs, the other parameters for the analysis (see Job_params) are allowed to default. InterProScan searches a protein sequence against the protein family and domain signature databases integrated into InterPro (see http://www.ebi.ac.uk/interpro/). A set of matches to the sig...

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

Viewed: 198 times | Downloaded: 129 times

Tags (5):

Original Uploader

Workflow EBI_InterProScan for Taverna 2 (2)

Created: 26/01/10 @ 14:45:46 | Last updated: 24/11/10 @ 10:04:09

Credits: User Stian Soiland-Reyes User Katy Wolstencroft User Paolo User Hamish McWilliam

Attributions: Workflow EBI_InterProScan for Taverna 2 Workflow EBI InterproScan T2 Workflow EBI_InterProScan Workflow EBI InterProScan

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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Perform an InterProScan analysis of a protein sequence using the EBI’s WSInterProScan service (see http://www.ebi.ac.uk/Tools/webservices/services/interproscan). The input sequence to use and the user e-mail address are inputs, the other parameters for the analysis (see Job_params) are allowed to default. InterProScan searches a protein sequence against the protein family and domain signature databases integrated into InterPro (see http://www.ebi.ac.uk/interpro/). A set of matches to t...

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

Viewed: 456 times | Downloaded: 210 times

Tags (6):

Original Uploader

Workflow workflow1 (1)

Created: 16/11/09 @ 14:12:30

Credits: User Jorgep

Attributions: Workflow EBI_InterProScan for Taverna 2

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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

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

Viewed: 47 times | Downloaded: 15 times

Tags (2):

Original Uploader

Workflow InterProScan (SOAP) (1)

Created: 03/12/10 @ 07:41:47 | Last updated: 03/12/10 @ 07:41:48

Attributions: Workflow EBI_InterProScan

License: Creative Commons Attribution 3.0 Unported License

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Perform an InterProScan search using the EMBL-EBI’s InterProScan (SOAP) service (see http://www.ebi.ac.uk/Tools/webservices/services/pfa/iprscan_soap). The query sequence to use is the input, the other parameters for the search are allowed to default.

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

Viewed: 33 times | Downloaded: 25 times

Tags (11):

Original Uploader

Workflow InterProScan (SOAP) (1)

Created: 03/12/10 @ 08:20:21 | Last updated: 03/12/10 @ 08:20:24

Credits: User Hamish McWilliam

Attributions: Workflow EBI_InterProScan Workflow InterProScan (SOAP)

License: Creative Commons Attribution 3.0 Unported License

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Perform an InterProScan search using the EMBL-EBI’s InterProScan (SOAP) service (see http://www.ebi.ac.uk/Tools/webservices/services/pfa/iprscan_soap). The query sequence to use is the input, the other parameters for the search are allowed to default.

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

Viewed: 30 times | Downloaded: 15 times

Tags (11):

Original Uploader

Workflow EBI_InterproScan_NewServices (2)

Created: 17/01/11 @ 16:08:48 | Last updated: 17/01/11 @ 16:12:40

Credits: User Katy Wolstencroft User Hamish McWilliam User Stian Soiland-Reyes

Attributions: Workflow EBI_InterProScan for Taverna 2 Workflow EBI_InterProScan for Taverna 2 Workflow EBI_InterProScan

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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This workflow performs an interproscan on provided sequencesThis workflow performs an interproscan at the EBI on sequences provided as input. The output is provided as text, xml or png. This workflow uses the new EBI services, which are asynchronous and require looping over the nested workflow (Status) until the workflow has finished. Many of the EBI services now work in this way, so you can use this workflow as an example of the invocation pattern and looping configuration.

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

Viewed: 77 times | Downloaded: 49 times

Tags (11):

Original Uploader

Workflow KEGG Pathways and Additional Information f... (2)

Created: 29/03/11 @ 11:16:17 | Last updated: 30/03/11 @ 16:09:01

Credits: User Morgan Taschuk

Attributions: Workflow extract_uniprot_embl_gi.xml

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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Takes in a tab-delimited BLAST file and finds additional information about the target proteins from KEGG, Gene Ontology, Interpro and PubMed.

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

Viewed: 51 times | Downloaded: 24 times

Tags (6):

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