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Items tagged with "transmembrane prediction" (7)

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Workflows (7)

Taverna 1 Original Uploader Hamish McWilliam	EBI_Phobius (v2) Created: 01/06/08 @ 11:08:45 \| Last updated: 02/06/08 @ 21:39:06 Credits: Hamish McWilliam License: Creative Commons Attribution 3.0 Unported License 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: 113 times \| Downloaded: 62 times Tags (8): bioinformatics \| ebi \| gff \| phobius \| protein \| protein annotation \| transmembrane \| transmembrane prediction	View Download (v2)
Taverna 1 Original Uploader Hamish McWilliam	EBI_InterProScan_tmhmm_signalp (v4) Created: 26/10/08 @ 20:50:10 \| Last updated: 01/04/11 @ 08:56:37 Credits: Hamish McWilliam Attributions: EBI_InterProScan License: Creative Commons Attribution 3.0 Unported License Note: the WSInterProScan web service used by this workflow is no longer available haveing been replaced by the EMBL-EBI's InterProScan (REST) (http://www.ebi.ac.uk/Tools/webservices/services/pfa/iprscan_rest) and InterProScan (SOAP)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: 203 times \| Downloaded: 83 times Tags (8): bioinformatics \| ebi \| gff \| interproscan \| protein \| protein annotation \| transmembrane \| transmembrane prediction	View Download (v4)
Taverna 1 Original Uploader Hamish McWilliam	Protein_alignment_transmembrane (v1) Created: 01/06/08 @ 12:20:29 Credits: Hamish McWilliam Attributions: EBI_FASTA EBI_ClustalW2 EBI_dbfetch_fetchBatch License: Creative Commons Attribution 3.0 Unported License 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: 190 times \| Downloaded: 57 times Tags (16): alignment \| bioinformatics \| clustal \| clustalw \| dbfetch \| ebi \| emboss \| emboss tmap \| FASTA \| multiple sequence alignment \| protein \| protein annotation \| sequence alignment \| sequence similarity search \| transmembrane \| transmembrane prediction	View Download (v1)
Taverna 1 Original Uploader Hamish McWilliam	tmap_single_sequence (v2) Created: 01/06/08 @ 14:27:12 \| Last updated: 02/06/08 @ 21:38:13 Credits: Hamish McWilliam Attributions: Sequence_or_ID License: Creative Commons Attribution 3.0 Unported License 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: 116 times \| Downloaded: 44 times Tags (9): bioinformatics \| ebi \| emboss \| emboss tmap \| gff \| protein \| protein annotation \| transmembrane \| transmembrane prediction	View Download (v2)
Taverna 1 Original Uploader Hamish McWilliam	Protein_transmembrane_prediction (v2) Created: 26/10/08 @ 21:16:10 \| Last updated: 01/04/11 @ 08:57:10 Credits: Hamish McWilliam Attributions: EBI_InterProScan_tmhmm_signalp EBI_Phobius tmap_single_sequence License: Creative Commons Attribution 3.0 Unported License 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: 320 times \| Downloaded: 91 times Tags (11): bioinformatics \| ebi \| emboss \| emboss tmap \| gff \| interproscan \| phobius \| protein \| protein annotation \| transmembrane \| transmembrane prediction	View Download (v2)
Taverna 2 Original Uploader Hamish McWilliam	InterProScan (SOAP) (v1) Created: 03/12/10 @ 07:41:47 \| Last updated: 03/12/10 @ 07:41:48 Attributions: EBI_InterProScan License: Creative Commons Attribution 3.0 Unported License 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: 24 times \| Downloaded: 17 times Tags (11): bioinformatics \| ebi \| interpro \| interproscan \| protein \| protein annotation \| protein domain \| protein family \| protein motif \| transmembrane \| transmembrane prediction	View Download (v1)
Taverna 1 Original Uploader Hamish McWilliam	InterProScan (SOAP) (v1) Created: 03/12/10 @ 08:20:21 \| Last updated: 03/12/10 @ 08:20:24 Credits: Hamish McWilliam Attributions: EBI_InterProScan InterProScan (SOAP) License: Creative Commons Attribution 3.0 Unported License 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: 23 times \| Downloaded: 11 times Tags (11): bioinformatics \| ebi \| interpro \| interproscan \| protein \| protein annotation \| protein domain \| protein family \| protein motif \| transmembrane \| transmembrane prediction	View Download (v1)