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Items tagged with "transmembrane" (7)

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Workflows (7)
Original Uploader

Workflow EBI_Phobius (2)

Created: 01/06/08 @ 11:08:45 | Last updated: 02/06/08 @ 21:39:06

Credits: User Hamish McWilliam

License: Creative Commons Attribution 3.0 Unported License

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The Phobius tool predicts transmembrane domains and signal peptide region from a protein sequence. This workflow uses the EBI's WSPhobius web service (see http://www.ebi.ac.uk/Tools/webservices/services/phobius) to access the tool. The predicted features are returned in a UniProtKB style feature listing.

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

Viewed: 118 times | Downloaded: 66 times

Tags (8):

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Note: the WSInterProScan web service used by this workflow is no longer available haveing been replaced by the EMBL-EBI's InterProScan (REST) (http://www.ebi.ac.uk/Tools/webservices/services/pfa/iprscan_rest) and InterProScan (SOAP)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

Created: 01/06/08 @ 12:20:29

Credits: User Hamish McWilliam

Attributions: Workflow EBI_FASTA Workflow EBI_ClustalW2 Workflow EBI_dbfetch_fetchBatch

License: Creative Commons Attribution 3.0 Unported License

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Transmembrane domain prediction using EMBOSS tmap with an input sequence alignment of homolouges: Sequence similarity search (SSS) to find homologues Fetch sequences of hits Multiple sequence alignment (MSA) of hit sequences EMBOSS tmap with alignment from 3. Uses the EBI web services: WSFasta (see http://www.ebi.ac.uk/Tools/webservices/services/fasta) WSDbfetch (see http://www.ebi.ac.uk/Tools/webservices/services/dbfetch) WSClustalW2 (see http://www.ebi.ac.uk/Tools/webservices/servic...

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

Viewed: 208 times | Downloaded: 59 times

Tags (16):

Original Uploader

Workflow tmap_single_sequence (2)

Created: 01/06/08 @ 14:27:12 | Last updated: 02/06/08 @ 21:38:13

Credits: User Hamish McWilliam

Attributions: Workflow Sequence_or_ID

License: Creative Commons Attribution 3.0 Unported License

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Simple workflow using tmap to find transmembrane regions, using a single sequence as input.

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

Viewed: 147 times | Downloaded: 45 times

Tags (9):

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 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):

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