Tag Results

Items tagged with "protein annotation" (16)

Note: some items may not be visible to you, due to viewing permissions.

Workflows (15)

Taverna 1 Original Uploader Hamish McWilliam	EBI_InterProScan (v3) Created: 26/10/08 @ 20:33:34 \| Last updated: 01/04/11 @ 08:52:28 Credits: Hamish McWilliam 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3.0 Unported License Note: the WSInterProScan web service used by this workflow is no longer available haveing been replaced by the EMBL-EBI's InterProScan (REST) (http://www.ebi.ac.uk/Tools/webservices/services/pfa/iprscan_rest) and InterProScan (SOAP)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. Perform an InterProScan ... Rating: 0.0 / 5 (0 ratings) \| Versions: 3 \| Reviews: 0 \| Comments: 1 \| Citations: 0 Viewed: 1237 times \| Downloaded: 374 times Tags (10): bioinformatics \| ebi \| gff \| go terms \| interpro \| interproscan \| protein annotation \| protein domain \| protein family \| protein motif	View Download (v3)
Taverna 1 Original Uploader Hamish McWilliam	EBI_InterProScan_with_prompts (v1) Created: 31/05/08 @ 11:40:34 \| Last updated: 01/04/11 @ 08:57:45 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3.0 Unported License Note: the WSInterProScan web service used by this workflow is no longer available haveing been replaced by the EMBL-EBI's InterProScan (REST) (http://www.ebi.ac.uk/Tools/webservices/services/pfa/iprscan_rest) and InterProScan (SOAP)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. Run an InterProScan anal... Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 84 times \| Downloaded: 50 times Tags (7): bioinformatics \| ebi \| go terms \| interpro \| interproscan \| protein annotation \| user_interaction	View Download (v1)
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 1 Original Uploader Hamish McWilliam	EBI_MPsrch (v1) Created: 02/06/08 @ 21:49:11 \| Last updated: 06/12/10 @ 10:38:42 Credits: Hamish McWilliam License: Creative Commons Attribution 3.0 Unported License Run a Smith-Waterman sequence search using the EBI’s WSMPsrch service (see http://www.ebi.ac.uk/Tools/webservices/services/mpsrch). Note: the WSMPsrch service used by this workflow was retired 27th January 2010. Equivalent functionality is available in the EBI's FASTA (REST or SOAP) and PSI-Search (REST or SOAP) services. Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 64 times \| Downloaded: 43 times Tags (7): bioinformatics \| ebi \| mpsrch \| protein \| protein annotation \| sequence similarity search \| smith-waterman	View Download (v1)
Taverna 1 Original Uploader Hamish McWilliam	Nucleotide_InterProScan (v4) Created: 26/10/08 @ 21:10:09 \| Last updated: 01/04/11 @ 08:54:21 Credits: Hamish McWilliam Attributions: EBI_InterProScan EBI_NCBI_BLAST Nucleotide_ORF_translation Fasta_string_to_fasta_list Sequence_or_ID 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. Run InterProScan using a... Rating: 0.0 / 5 (0 ratings) \| Versions: 4 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 358 times \| Downloaded: 119 times Tags (11): bioinformatics \| BLAST \| ebi \| interpro \| interproscan \| ncbi blast \| nucleotide sequence \| nucleotide translation \| open reading frame \| protein \| protein annotation	View Download (v4)
Taverna 1 Original Uploader Hamish McWilliam	EBI_Blast2InterPro (v2) Created: 26/10/08 @ 20:45:45 \| Last updated: 01/04/11 @ 08:55:49 Credits: Hamish McWilliam Attributions: EBI_WU-BLAST EBI_dbfetch_fetchBatch Fasta_string_to_fasta_list 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. Perform a BLAST search a... Rating: 0.0 / 5 (0 ratings) \| Versions: 2 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 245 times \| Downloaded: 94 times Tags (11): bioinformatics \| BLAST \| dbfetch \| ebi \| go terms \| interpro \| interproscan \| protein \| protein annotation \| sequence similarity search \| wu-blast	View Download (v2)
Taverna 1 Original Uploader Hamish McWilliam	EBI_Fetch_InterPro_Matches_UniParc (v1) Created: 08/06/08 @ 14:08:47 Credits: Hamish McWilliam License: Creative Commons Attribution 3.0 Unported License 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: 65 times \| Downloaded: 34 times Tags (9): bioinformatics \| ebi \| interpro \| protein \| protein annotation \| srs \| uniparc \| uniprot archive \| upi	View Download (v1)
Taverna 1 Original Uploader Hamish McWilliam	EBI_IntAct (v1) Created: 09/07/08 @ 06:01:17 Credits: Hamish McWilliam License: Creative Commons Attribution 3.0 Unported License Find protein binary interactions using the EBI's IntAct service. See http://www.ebi.ac.uk/intact/ for further details. Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 117 times \| Downloaded: 57 times Tags (7): binary \| bioinformatics \| ebi \| intact \| protein \| protein annotation \| protein interaction	View Download (v1)
Taverna 1 Original Uploader José Manuel Rodríguez	runFunCUT (v1) Created: 03/10/08 @ 10:54:45 \| Last updated: 03/10/08 @ 11:49:17 Credits: José Manuel Rodríguez License: Creative Commons Attribution-Share Alike 3.0 Unported License MOBY Web Services (synchronous and asynchronous) that describe the FunCUT method. Is recommended use asynchronous MOBY services because the method needs huge range of time. FunCUT Method Short Description: Annotates homologous sequences and includes new features related to the specific identification of protein subfamilies (orthologous groups) FunCUT (Abascal and Valencia, 2003. PROTEINS: Structure, Function, and Genetics 53:683– 692 (2003)) is application based on the study... Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 111 times \| Downloaded: 0 times Tags (4): bioinformatics \| inb \| protein annotation \| protein family	View
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)