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Items tagged with "transmembrane" (5)

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Taverna 1

Original Uploader

Hamish McWilliam

EBI_Phobius (v2)

Created: 01/06/08 @ 11:08:46 | Last updated: 02/06/08 @ 21:39:07

Credits: Hamish McWilliam

License: Creative Commons Attribution 3.0 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: 312 times | Downloaded: 260 times

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Taverna 1

Original Uploader

Hamish McWilliam

EBI_InterProScan_tmhmm_signalp (v4)

Created: 01/06/08 @ 11:21:46 | Last updated: 26/10/08 @ 20:50:11

Credits: Hamish McWilliam

Attributions: EBI_InterProScan

License: Creative Commons Attribution 3.0 License

Use the TMHMM and SignalP methods of InterProScan to perform transmembrane and signal peptide prediction. The EBI's InterProScan web service (see http://www.ebi.ac.uk/Tools/webservices/services/interproscan) is used.

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

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Taverna 1

Original Uploader

Hamish McWilliam

Protein_alignment_transmembrane (v1)

Created: 01/06/08 @ 12:20:30 | Last updated: 01/06/08 @ 12:20:31

Credits: Hamish McWilliam

Attributions: EBI_FASTA EBI_ClustalW2 EBI_dbfetch_fetchBatch

License: Creative Commons Attribution 3.0 License

Transmembrane domain prediction using EMBOSS tmap with an input sequence alignment of homolouges: 1. Sequence similarity search (SSS) to find homologues 2. Fetch sequences of hits 3. Multiple sequence alignment (MSA) of hit sequences 4. EMBOSS tmap with alignment from 3. Uses the EBI web services: 1. WSFasta (see http://www.ebi.ac.uk/Tools/webservices/services/fasta) 2. WSDbfetch (see http://www.ebi.ac.uk/Tools/webservices/services/dbfetch) 3. WSClustalW2 (see http://www.ebi.ac.uk/Tools/webs...

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

Viewed: 249 times | Downloaded: 281 times

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Taverna 1

Original Uploader

Hamish McWilliam

tmap_single_sequence (v2)

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

Credits: Hamish McWilliam

Attributions: Sequence_or_ID

License: Creative Commons Attribution 3.0 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: 286 times | Downloaded: 270 times

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Taverna 1

Original Uploader

Hamish McWilliam

Protein_transmembrane_prediction (v2)

Created: 01/06/08 @ 17:49:32 | Last updated: 26/10/08 @ 21:16:10

Credits: Hamish McWilliam

Attributions: EBI_InterProScan_tmhmm_signalp EBI_Phobius tmap_single_sequence

License: Creative Commons Attribution 3.0 License

Transmembrane and signal peptide prediction using three methods: 1. EMBOSS tmap with a single sequence. Uses Soaplab tmap. 2. Phobius. Uses EBI's WSPhobius web service. 3. TMHMM and SignalP. Uses the TMHMM and SignalP methods of InterProScan via the EBI's WSInterProScan service. The results of the three methods are converted into GFF format and collated.

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

Viewed: 345 times | Downloaded: 310 times

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