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Items tagged with "ebi" (68)

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Workflows (66)

Taverna 1 Original Uploader Hamish McWilliam	EBI_WU-BLAST (v1) Created: 30/05/08 @ 22:47:18 \| Last updated: 06/12/10 @ 10:51:04 Credits: Hamish McWilliam License: Creative Commons Attribution 3.0 Unported License Perform a BLAST search using the EBI's WSWUBlast service (see http://www.ebi.ac.uk/Tools/webservices/services/wublast). The default parameters search UniProtKB using blastp. To change the job parameters see Job_params. Note: the WSWUBlast service used by this workflow is deprecated as of 21st September 2010 and should not be used in any new development. This service is will be retired during 2011. EBI's replacement WU-BLAST services (REST or SOAP) should be used instead. Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 208 times \| Downloaded: 78 times Tags (5): bioinformatics \| BLAST \| ebi \| sequence similarity search \| wu-blast	View Download (v1)
Taverna 1 Original Uploader Hamish McWilliam	EBI WU-BLAST with program and database selection prompts. (v3) Created: 04/07/09 @ 11:39:54 \| Last updated: 06/12/10 @ 10:56:44 Credits: Hamish McWilliam Attributions: EBI_WU-BLAST License: Creative Commons Attribution 3.0 Unported License Run a BLAST analysis using the EBI's WSWUBlast service (see http://www.ebi.ac.uk/Tools/webservices/services/wublast). This workflow wraps the EBI_WU-BLAST workflow to provide a basic user interface which prompts for the required inputs: sequence, database, BLAST program and user e-mail. Other parameters (e.g. matrix, sort, gap penalties, etc.) are allowed to default. The values presented in the selection menus for the program and database are obtained from the service, using the provided me... Rating: 0.0 / 5 (0 ratings) \| Versions: 3 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 169 times \| Downloaded: 82 times Tags (6): bioinformatics \| BLAST \| ebi \| sequence similarity search \| user_interaction \| wu-blast	View Download (v3)
Taverna 1 Original Uploader Hamish McWilliam	EBI_FASTA (v1) Created: 30/05/08 @ 23:50:46 \| Last updated: 06/12/10 @ 10:52:25 Credits: Hamish McWilliam License: Creative Commons Attribution 3.0 Unported License Run a FASTA or SSEARCH sequence similarity search using the EBI's WSFasta service (see http://www.ebi.ac.uk/Tools/webservices/services/fasta). Note: the WSFasta service used by this workflow is deprecated as of 21st September 2010 and should not be used in any new development. This service is will be retired during 2011. EBI's replacement FASTA services (REST or SOAP) should be used instead. Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 85 times \| Downloaded: 49 times Tags (6): bioinformatics \| ebi \| FASTA \| sequence similarity search \| smith-waterman \| ssearch	View Download (v1)
Taverna 1 Original Uploader Hamish McWilliam	EBI FASTA with prompts (v3) Created: 30/05/08 @ 23:53:16 \| Last updated: 06/12/10 @ 10:53:23 Credits: Hamish McWilliam Attributions: EBI_FASTA License: Creative Commons Attribution 3.0 Unported License Run a FASTA analysis using the EBI’s WSFasta service (see http://www.ebi.ac.uk/Tools/webservices/services/fasta). This workflow wraps the EBI_FASTA workflow to provide a basic user interface which prompts for the required inputs: sequence, database, FASTA program and user e-mail. Other parameters (e.g. matrix, gap penalties, etc.) are allowed to default. Note: the WSFasta service used by this workflow is deprecated as of 21st September 2010 and should not be used in any new developme... Rating: 0.0 / 5 (0 ratings) \| Versions: 3 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 86 times \| Downloaded: 44 times Tags (7): bioinformatics \| ebi \| FASTA \| sequence similarity search \| smith-waterman \| ssearch \| user_interaction	View Download (v3)
Taverna 1 Original Uploader Hamish McWilliam	EBI_NCBI_BLAST (v1) Created: 31/05/08 @ 08:38:46 \| Last updated: 06/12/10 @ 10:54:16 Credits: Hamish McWilliam License: Creative Commons Attribution 3.0 Unported License Perform a BLAST search using the EBI’s WSNCBIBlast service (see http://www.ebi.ac.uk/Tools/webservices/services/ncbiblast). The query sequence, database to search and BLAST program to use are inputs, the other parameters for the search (see Job_params) are allowed to default. Note: the WSNCBIBlast service used by this workflow is deprecated as of 21st September 2010 and should not be used in any new development. This service is will be retired during 2011. EBI's replacement NCBI BLA... Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 1 \| Citations: 0 Viewed: 312 times \| Downloaded: 154 times Tags (6): bioinformatics \| BLAST \| blastall \| ebi \| ncbi blast \| sequence similarity search	View Download (v1)
Taverna 1 Original Uploader Hamish McWilliam	EBI_NCBI_BLAST_with_prompts (v1) Created: 31/05/08 @ 08:40:29 \| Last updated: 06/12/10 @ 10:55:09 Credits: Hamish McWilliam Attributions: EBI_NCBI_BLAST License: Creative Commons Attribution 3.0 Unported License Run a BLAST analysis using the EBI’s WSNCBIBlast service (see http://www.ebi.ac.uk/Tools/webservices/services/ncbiblast). This workflow wraps the EBI_NCBI_BLAST workflow to provide a basic user interface which prompts for the required inputs: sequence, database, BLAST program and user e-mail. Other parameters (e.g. matrix, sort, gap penalties, etc.) are allowed to default. Note: the WSNCBIBlast service used by this workflow is deprecated as of 21st September 2010 and should not be use... Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 109 times \| Downloaded: 73 times Tags (7): bioinformatics \| BLAST \| blastall \| ebi \| ncbi blast \| sequence similarity search \| user_interaction	View Download (v1)
Taverna 1 Original Uploader Hamish McWilliam	EBI_ClustalW2 (v2) Created: 07/04/09 @ 20:06:03 \| Last updated: 06/12/10 @ 11:00:19 Credits: Hamish McWilliam License: Creative Commons Attribution 3.0 Unported License Perform a ClustalW multiple sequence alignment using the EBI’s WSClustalW2 service (see http://www.ebi.ac.uk/Tools/webservices/services/clustalw2). The set of sequences to align are the input, the other parameters for the search (see Job_params) are allowed to default. Note: the WSClustalW2 service used by this workflow is deprecated as of 21st September 2010 and should not be used in any new development. This service is will be retired during 2011. EBI's replacement ClustalW2 servi... Rating: 0.0 / 5 (0 ratings) \| Versions: 2 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 506 times \| Downloaded: 240 times Tags (7): alignment \| bioinformatics \| clustal \| clustalw \| ebi \| multiple sequence alignment \| sequence alignment	View Download (v2)
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_ClustalW2_phylogentic_tree (v2) Created: 07/04/09 @ 20:09:32 Credits: Hamish McWilliam License: Creative Commons Attribution 3.0 Unported License Create a Neighbor-joining phylogenetic tree, with Kimura distance corrections, from a sequence alignment using the EBI's WSClustalW2 service (see http://www.ebi.ac.uk/Tools/webservices/services/clustalw2). Rating: 4.0 / 5 (1 rating) \| Versions: 2 \| Reviews: 1 \| Comments: 1 \| Citations: 0 Viewed: 280 times \| Downloaded: 102 times Tags (7): bioinformatics \| clustal \| clustalw \| ebi \| neighbor-joining \| phylogenetic tree \| tree	View Download (v2)
Taverna 1 Original Uploader Hamish McWilliam	EBI_ClustalW_alignment_tree (v2) Created: 31/05/08 @ 13:53:04 \| Last updated: 03/12/10 @ 13:34:43 Credits: Hamish McWilliam Attributions: EBI_ClustalW2 EBI_ClustalW2_phylogentic_tree License: Creative Commons Attribution 3.0 Unported License Given a set of sequences perform an multiple sequence alignment and from the multiple alignment derive a phylogenetic tree. The popular ClustalW program (see http://www.clustal.org/), as implemented in the EBI's WSClustalW2 service (see http://www.ebi.ac.uk/Tools/webservices/services/clustalw2) is used to perform both tasks. Rating: 0.0 / 5 (0 ratings) \| Versions: 2 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 176 times \| Downloaded: 83 times Tags (10): alignment \| bioinformatics \| clustal \| clustalw \| ebi \| multiple sequence alignment \| neighbor-joining \| phylogenetic tree \| sequence alignment \| tree	View Download (v2)
Taverna 1 Original Uploader Hamish McWilliam	EBI_blastpgp_PSI-BLAST (v1) Created: 31/05/08 @ 14:39:22 Credits: Hamish McWilliam License: Creative Commons Attribution 3.0 Unported License Perform a PSI-BLAST iterative search using the EBI’s WSBlastpgp service (see http://www.ebi.ac.uk/Tools/webservices/services/blastpgp). The query sequence, database to search and users e-mail address are inputs, the other parameters for the search (see Job_params) are allowed to default. In most cases you will probably want to adjust the expectation thresholds and the maximum number of iterations for your specific query sequence and the database being searched. Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 123 times \| Downloaded: 61 times Tags (7): bioinformatics \| BLAST \| blastpgp \| ebi \| ncbi blast \| PSI-BLAST \| sequence similarity search	View Download (v1)
Taverna 1 Original Uploader Hamish McWilliam	EBI_dbfetch_fetchBatch (v1) Created: 31/05/08 @ 20:59:46 Credits: Hamish McWilliam License: Creative Commons Attribution 3.0 Unported License From a list of sequence entry identifiers and a database name, fetch the sequences in fasta format using EBI's WSDbfetch service (see http://www.ebi.ac.uk/Tools/webservices/wsdl/WSDbfetch.wsdl). Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 103 times \| Downloaded: 70 times Tags (3): bioinformatics \| dbfetch \| ebi	View Download (v1)
Taverna 1 Original Uploader Hamish McWilliam	Protein_search_fetch_align_tree (v2) Created: 07/04/09 @ 20:13:19 Credits: Hamish McWilliam Attributions: EBI_ClustalW2 EBI_ClustalW2_phylogentic_tree EBI_dbfetch_fetchBatch EBI_WU-BLAST License: Creative Commons Attribution 3.0 Unported License An implmentation of the classical sequence analysis workflow: Find homologues (sequence similarity search) Fetch homologues Align homologues (multiple sequence alignment) Produce phylogenetic tree In this implementation the EBI webservices are used: WU-BLAST (WSWUBlast) blastp vs. UniProtKB dbfetch (WSDbfetch) ClustalW (WSClustalW2) ClustalW (WSClustalW2) Note: this version does not add the inital query sequence to the alignment, and so is most useful when used with the identifers... Rating: 0.0 / 5 (0 ratings) \| Versions: 2 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 419 times \| Downloaded: 140 times Tags (15): alignment \| bioinformatics \| BLAST \| clustal \| clustalw \| dbfetch \| ebi \| multiple sequence alignment \| neighbor-joining \| phylogenetic tree \| protein \| sequence alignment \| sequence similarity search \| tree \| wu-blast	View Download (v2)
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	Sequence_or_ID (v1) Created: 01/06/08 @ 14:15:12 Credits: Hamish McWilliam License: Creative Commons Attribution 3.0 Unported License Given a sequence or sequence entry identifer (e.g. uniprot:wap_rat), return the sequence in fasta format. If a sequence identifier, in database:identifier format, is input the EBI's WSDbfetch web service (see http://www.ebi.ac.uk/Tools/webservices/services/dbfetch) is used to retrive the sequence in fasta format. Otherwise the input is assumed to be a sequence and if passed through the Soaplab EMBOSS seqret service to force the sequence into fasta format. Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 144 times \| Downloaded: 60 times Tags (6): bioinformatics \| dbfetch \| ebi \| emboss \| emboss seqret \| sequence retrieval	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: 319 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_Kalign (v1) Created: 02/06/08 @ 21:28:56 \| Last updated: 06/12/10 @ 11:39:52 Credits: Hamish McWilliam License: Creative Commons Attribution 3.0 Unported License Multiple sequence alignment using the Kalign tool. This workflow uses the EBI's WSKalign service (see http://www.ebi.ac.uk/Tools/webservices/services/kalign) to access the Kalign tool. The set of sequences to align and the molecule type (protein or nucleic acid) are the input, the other parameters for the search (see Job_params) are allowed to default. Note: the WSKalign service used by this workflow is deprecated as of 21st September 2010 and should not be used in any new development. Thi... Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 73 times \| Downloaded: 45 times Tags (6): alignment \| bioinformatics \| ebi \| kalign \| multiple sequence alignment \| sequence alignment	View Download (v1)
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	EBI_MAFFT (v1) Created: 03/06/08 @ 05:55:43 \| Last updated: 06/12/10 @ 11:38:58 Credits: Hamish McWilliam License: Creative Commons Attribution 3.0 Unported License Perform a multiple sequence alignment using the MAFFT tool (see http://align.bmr.kyushu-u.ac.jp/mafft/software/). The EBI's WSMafft web service (see http://www.ebi.ac.uk/Tools/webservices/services/mafft) is used to access to tool. Note: the WSMafft service used by this workflow is deprecated as of 21st September 2010 and should not be used in any new development. This service is will be retired during 2011. EBI's replacement MAFFT services (REST or SOAP) should be used instead. Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 94 times \| Downloaded: 55 times Tags (6): alignment \| bioinformatics \| ebi \| mafft \| multiple sequence alignment \| sequence alignment	View Download (v1)
Taverna 1 Original Uploader Hamish McWilliam	EBI_ScanPS (v1) Created: 03/06/08 @ 05:57:09 \| Last updated: 06/12/10 @ 10:37:50 Credits: Hamish McWilliam License: Creative Commons Attribution 3.0 Unported License Perform a Smith-Waterman sequence similarity search using the ScanPS tool (see http://www.compbio.dundee.ac.uk/Software/Scanps/scanps.html). In the case the EBI's WSScanPS web service (see http://www.ebi.ac.uk/Tools/webservices/services/scanps) is used to run the tool. Note: the WSScanPS 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: 58 times \| Downloaded: 38 times Tags (6): bioinformatics \| ebi \| protein \| scanps \| sequence similarity search \| smith-waterman	View Download (v1)
Taverna 1 Original Uploader Hamish McWilliam	EBI_MUSCLE (v1) Created: 03/06/08 @ 06:16:22 \| Last updated: 06/12/10 @ 11:04:03 Credits: Hamish McWilliam License: Creative Commons Attribution 3.0 Unported License Perform a multiple sequence alignment using the MUSCLE tool (see http://www.drive5.com/muscle/). The EBI's WSMuscle web service (see http://www.ebi.ac.uk/Tools/webservices/services/muscle) is used. Note: the WSMuscle service used by this workflow is deprecated as of 21st September 2010 and should not be used in any new development. This service is will be retired during 2011. EBI's replacement MUSCLE services (REST or SOAP) should be used instead. Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 109 times \| Downloaded: 57 times Tags (6): alignment \| bioinformatics \| ebi \| multiple sequence alignment \| muscle \| sequence alignment	View Download (v1)
Taverna 1 Original Uploader Hamish McWilliam	EBI_TCoffee (v1) Created: 03/06/08 @ 06:31:37 \| Last updated: 06/12/10 @ 11:02:53 Credits: Hamish McWilliam License: Creative Commons Attribution 3.0 Unported License Perform a multiple sequence alignment using T-Coffee (see http://www.tcoffee.org/). The EBI's WSTCoffee web service (see http://www.ebi.ac.uk/Tools/webservices/services/tcoffee) is used. Note: the WSTCoffee service used by this workflow is deprecated as of 21st September 2010 and should not be used in any new development. This service is will be retired during 2011. EBI's replacement T-COFFEE services (REST or SOAP) should be used instead. Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 127 times \| Downloaded: 61 times Tags (6): alignment \| bioinformatics \| ebi \| multiple sequence alignment \| sequence alignment \| t-coffee	View Download (v1)
Taverna 1 Original Uploader Hamish McWilliam	EBI_MaxSprout (v2) Created: 05/06/08 @ 21:44:00 \| Last updated: 06/06/08 @ 05:58:16 Credits: Hamish McWilliam Attributions: Structure_or_ID License: Creative Commons Attribution 3.0 Unported License Generation of protein backbone and side chain co-ordinates from a C(alpha) trace using the MaxSprout tool. The EBI's WSMaxsprout service (see http://www.ebi.ac.uk/Tools/webservices/services/maxsprout) is used to access the tool. Rating: 0.0 / 5 (0 ratings) \| Versions: 2 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 62 times \| Downloaded: 40 times Tags (6): backbone \| bioinformatics \| ebi \| pdb \| protein \| structure	View Download (v2)
Taverna 1 Original Uploader Hamish McWilliam	Structure_or_ID (v1) Created: 06/06/08 @ 05:57:31 Credits: Hamish McWilliam License: Creative Commons Attribution 3.0 Unported License Given a structure or structure entry identifer (e.g. PDB:1crn), return the structure in PDB format. If a structure identifier, in database:identifier format, is input the EBI's WSDbfetch web service (see http://www.ebi.ac.uk/Tools/webservices/services/dbfetch) is used to retrive the structure in PDB format. Otherwise the input is assumed to be a formated structure and is passed through to the output. Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 379 times \| Downloaded: 37 times Tags (8): bioinformatics \| dbfetch \| ebi \| pdb \| protein \| protein structure \| structure \| structure retrieval	View Download (v1)
Taverna 1 Original Uploader Hamish McWilliam	Nucleotide_ORF_translation (v1) Created: 06/06/08 @ 20:13:04 Credits: Hamish McWilliam Attributions: Sequence_or_ID License: Creative Commons Attribution 3.0 Unported License From a nucleotide sequence get the protein translations of the open reading frames (stop to stop) that are longer than a specifed minimum length. EMBOSS getorf is used to find the ORFs and perform the translations. The getorf tool is accessed via Soaplab (see http://www.ebi.ac.uk/Tools/webservices/soaplab/overview). Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 183 times \| Downloaded: 96 times Tags (8): bioinformatics \| ebi \| emboss \| emboss getorf \| nucleotide sequence \| nucleotide translation \| open reading frame \| ORF	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: 357 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	Sequence_or_ID_or_GI (v1) Created: 07/06/08 @ 16:58:14 Credits: Hamish McWilliam Attributions: Structure_or_ID License: Creative Commons Attribution 3.0 Unported License Get a sequence in fasta format given one of: An NCBI GI number (e.g. 75251068). An entry identifier in database:identifier format (e.g. uniprot:Q96247). 3. A sequence entry in a format supported by EMBOSS seqret. Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 118 times \| Downloaded: 60 times Tags (9): bioinformatics \| dbfetch \| ebi \| efetch \| fasta format \| gi \| ncbi \| sequence identifier \| sequence retrieval	View Download (v1)
Taverna 1 Original Uploader Hamish McWilliam	EBI_DaliLite (v1) Created: 07/06/08 @ 17:16:37 Credits: Hamish McWilliam License: Creative Commons Attribution 3.0 Unported License Pairwise structure comparison using the DaliLite tool. The EBI's WSDaliLite web service (see http://www.ebi.ac.uk/Tools/webservices/services/dalilite) is used to access the tool. Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 75 times \| Downloaded: 49 times Tags (7): bioinformatics \| ebi \| pairwise structure comparison \| pdb \| protein \| protein structure \| structure	View Download (v1)
Taverna 1 Original Uploader Hamish McWilliam	EBI_PICR_Sequence_to_UniParc_and_InterPro (v2) Created: 08/06/08 @ 13:53:39 \| Last updated: 08/06/08 @ 14:10:02 Credits: Hamish McWilliam Attributions: EBI_dbfetch_UniParc EBI_Fetch_InterPro_Matches_UniParc EBI_PICR_Sequence_to_ID License: Creative Commons Attribution 3.0 Unported License 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: 158 times \| Downloaded: 57 times Tags (13): bioinformatics \| dbfetch \| ebi \| fasta format \| gi \| interpro \| picr \| protein \| sequence identifier \| sequence retrieval \| uniparc \| uniprot archive \| upi	View Download (v2)
Taverna 1 Original Uploader Hamish McWilliam	EBI_PICR_Sequence_to_ID (v1) Created: 08/06/08 @ 14:03:07 Credits: Hamish McWilliam License: Creative Commons Attribution 3.0 Unported License Map a protein sequence to the known identifiers of identical sequences. Uses the EBI's PICR web service (see http://www.ebi.ac.uk/Tools/picr/) to perform the mapping. Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 72 times \| Downloaded: 39 times Tags (9): bioinformatics \| ebi \| gi \| picr \| protein \| sequence identifier \| uniparc \| uniprot archive \| upi	View Download (v1)
Taverna 1 Original Uploader Hamish McWilliam	EBI_dbfetch_UniParc (v1) Created: 08/06/08 @ 14:05:40 Credits: Hamish McWilliam License: Creative Commons Attribution 3.0 Unported License From a list of UniParc entry identifers get the complete entries using the EBI's WSDbfetch service (see http://www.ebi.ac.uk/Tools/webservices/services/dbfetch). Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 53 times \| Downloaded: 33 times Tags (9): bioinformatics \| dbfetch \| ebi \| protein \| sequence identifier \| sequence retrieval \| uniparc \| uniprot archive \| upi	View Download (v1)
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_CENSOR (v2) Created: 17/06/08 @ 20:42:46 \| Last updated: 25/06/08 @ 06:16:03 Credits: Hamish McWilliam License: Creative Commons Attribution 3.0 Unported License The CENSOR tool identifies and masks simple and complex sequence repeats found in nucleotide and protein sequences. This workflow uses the EBI's WSCensor web service (see http://www.ebi.ac.uk/Tools/webservices/services/censor) to access the tool. Rating: 4.0 / 5 (1 rating) \| Versions: 2 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 152 times \| Downloaded: 50 times Tags (6): bioinformatics \| censor \| ebi \| nucleotide sequence \| protein \| repeat masking	View Download (v2)
Taverna 1 Original Uploader Hamish McWilliam	EBI_CiteXplore (v1) Created: 09/07/08 @ 04:53:56 Credits: Hamish McWilliam License: Creative Commons Attribution 3.0 Unported License Perform a literature search using the EBI's CiteXplore service (http://www.ebi.ac.uk/citexplore/), and get the results in a minimal XML format containing the citation information (i.e. title, author, journal, etc.), the identifier of the citation in the source database (PubMed/Medline, Agricola, Patent Abstracts, CBA, CiteSeer, etc.) and information about abstract and full article availablity including URLs. Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 62 times \| Downloaded: 34 times Tags (9): agricola \| citation \| citexplore \| doi \| ebi \| literature \| literature search \| medline \| pubmed	View Download (v1)
Taverna 1 Original Uploader Hamish McWilliam	EBI_Whatizit (v1) Created: 09/07/08 @ 05:14:28 Credits: Hamish McWilliam License: Creative Commons Attribution 3.0 Unported License Perform a text-mining analysis of an input text document using the EBI's Whatizit tool (http://www.ebi.ac.uk/webservices/whatizit/info.jsf). Whatizit provides a number of text-mining pipelines which can can detect various terms of biological interest in text documents. For example finding gene names and mapping them to UniProtKB identifiers, finding chemical terms and mapping them to ChEBI, etc. Rating: 5.0 / 5 (1 rating) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 177 times \| Downloaded: 62 times Tags (5): ebi \| text mining \| text mining; term extraction; entity recognition \| text_mining \| whatizit	View Download (v1)
Taverna 1 Original Uploader Hamish McWilliam	EBI_OLS_TermInfo (v1) Created: 09/07/08 @ 05:36:40 Credits: Hamish McWilliam License: Creative Commons Attribution 3.0 Unported License Get details of an ontology term given its identifer. This workflow uses the EBI's Ontology Lookup Service (OLS) to get the details of the ontology term. The OLS suports a wide range of biological and bioinformatic ontologies. See http://www.ebi.ac.uk/ontology-lookup/ for more information. Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 86 times \| Downloaded: 43 times Tags (9): bioinformatics \| ebi \| gene ontology \| GO \| go terms \| ols \| ontologies \| ontology \| ontology lookup service	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)
BioExtract Server Original Uploader Carol Lushbough	Nucleotide InterProScan for the BioExtract Server (v3) Created: 16/04/09 @ 15:26:57 \| Last updated: 01/07/09 @ 08:32:34 Credits: Carol Lushbough Hamish McWilliam Attributions: Nucleotide_InterProScan License: Creative Commons Attribution-Share Alike 3.0 Unported License This workflow can be downloaded and imported into the BioExtract Server at bioextract.org. This workflow is a BioExtract Server process similar to the Nucleotide InterProScan workflow designed and implement in Taverna by Hamish McWilliams. The InterProScan tool (http://www.ebi.ac.uk/Tools/InterProScan/) searches a protein sequence against a selection of protein domain, feature and family signature databases, and integrates the results giving potential assignments to InterPro entries and Gen... Rating: 0.0 / 5 (0 ratings) \| Versions: 3 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 149 times \| Downloaded: 89 times Tags (5): bioinformatics \| BLAST \| blastp \| ebi \| interproscan	View Download (v3)
BioExtract Server Original Uploader Carol Lushbough	Multiple Protein Alignment Profiling(1) (v4) Created: 13/01/10 @ 18:52:45 \| Last updated: 17/11/10 @ 14:13:20 Credits: Carol Lushbough Alan Williams Attributions: A workflow version of the EMBOSS tutorial License: Creative Commons Attribution-Share Alike 3.0 Unported License Designed from an example workflow at Traverna, this workflow retrieves a set of sequences from UniProt, then simultaneously scans for transmembrane regions and performs a multiple alignment using EMMA. The alignment is then plotted to a set of PNG images, followed by a profile analysis using prophecy and prophet tools. Rating: 0.0 / 5 (0 ratings) \| Versions: 4 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 152 times \| Downloaded: 60 times Tags (7): alignment \| ebi \| emma \| genomics \| prettyplot \| profile \| tmap	View Download (v4)
Triana Original Uploader Hamish McWilliam	EBI_dbfetch_fetchData (v1) Created: 28/08/09 @ 11:45:50 \| Last updated: 28/08/09 @ 11:49:08 Credits: Hamish McWilliam License: Creative Commons Attribution 3.0 Unported License Sample workflow illustrating the use of the EBI's WSDbfetch service in Triana. Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 1 \| Citations: 0 Viewed: 54 times \| Downloaded: 29 times Tags (4): bioinformatics \| dbfetch \| ebi \| sequence retrieval	View Download (v1)
Triana Original Uploader Hamish McWilliam	EBI_dbfetch_fetchBatch (v1) Created: 28/08/09 @ 11:55:10 Credits: Hamish McWilliam License: Creative Commons Attribution 3.0 Unported License Sample workflow illustrating the use of EBI's WSDbfetch service with Triana. Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 59 times \| Downloaded: 18 times Tags (5): bioinformatics \| dbfetch \| ebi \| example \| structure retrieval	View Download (v1)
Taverna 2 Original Uploader Francois Belleau	Triplify EB-Eye databases list from EBI [myexperiments:eb-eye_namespace2rdf2rdf] (v1) Created: 30/11/09 @ 20:58:14 \| Last updated: 30/11/09 @ 20:59:49 Credits: Francois Belleau License: Creative Commons Attribution-Share Alike 3.0 Unported License TAG: knowledgescope, eb-eye, bio2rdf, banff_manifesto, rdf, ebi, soap Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 27 times \| Downloaded: 15 times Tags (7): banff_manifesto \| bio2rdf \| cognoscope \| eb-eye \| ebi \| rdf \| soap	View Download (v1)
Taverna 2 Original Uploader Francois Belleau	Triplify namespace list from global search services from EBI, KEGG, NCBI and UniProt [myexperiment:search_services_namespace2rdf] (v1) Created: 30/11/09 @ 21:38:23 \| Last updated: 30/11/09 @ 21:44:57 Credits: Francois Belleau License: Creative Commons Attribution-Share Alike 3.0 Unported License No description Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 22 times \| Downloaded: 13 times Tags (7): banff_manifesto \| bio2rdf \| cognoscope \| ebi \| kegg \| ncbi \| uniprot	View Download (v1)
Taverna 1 Original Uploader Hamish McWilliam	NCBI BLAST (SOAP) (v1) Created: 29/11/10 @ 20:46:58 \| Last updated: 29/11/10 @ 20:47:00 Credits: Hamish McWilliam Attributions: EBI_NCBI_BLAST NCBI BLAST (SOAP) License: Creative Commons Attribution 3.0 Unported License Perform a BLAST search using the EMBL-EBI’s NCBI BLAST (SOAP) service (see http://www.ebi.ac.uk/Tools/webservices/services/sss/ncbi_blast_soap). The query sequence, database to search and BLAST program to use are inputs, 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: 29 times \| Downloaded: 16 times Tags (7): bioinformatics \| BLAST \| blastall \| blastp \| ebi \| ncbi blast \| sequence similarity search	View Download (v1)
Taverna 2 Original Uploader Hamish McWilliam	NCBI BLAST (SOAP) (v1) Created: 29/11/10 @ 20:03:13 \| Last updated: 29/11/10 @ 20:03:14 Attributions: EBI_NCBI_BLAST NCBI BLAST (SOAP) License: Creative Commons Attribution 3.0 Unported License Perform a BLAST search using the EMBL-EBI’s NCBI BLAST (SOAP) service (see http://www.ebi.ac.uk/Tools/webservices/services/sss/ncbi_blast_soap). The query sequence, database to search and BLAST program to use are inputs, 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: 44 times \| Downloaded: 61 times Tags (7): bioinformatics \| BLAST \| blastall \| blastp \| ebi \| ncbi blast \| sequence similarity search	View Download (v1)
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)
Taverna 2 Original Uploader Hamish McWilliam	EMBL-EBI ClustalW2 (SOAP) (v1) Created: 06/12/10 @ 13:16:52 Attributions: EBI_ClustalW2 License: Creative Commons Attribution 3.0 Unported License Perform a ClustalW2 alignment using the EMBL-EBI’s ClustalW2 (SOAP) service (see http://www.ebi.ac.uk/Tools/webservices/services/msa/clustalw2_soap). Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 22 times \| Downloaded: 19 times Tags (7): alignment \| bioinformatics \| clustal \| clustalw \| ebi \| multiple sequence alignment \| sequence alignment	View Download (v1)
Taverna 2 Original Uploader Katy Wolstencroft	EBI_NCBI_BLAST (v1) Created: 17/01/11 @ 12:51:58 \| Last updated: 17/01/11 @ 12:52:03 Credits: Katy Wolstencroft Hamish McWilliam Attributions: EBI_NCBI_BLAST License: Creative Commons Attribution-Share Alike 3.0 Unported License This workflow performs an NCBI blast at the EBI. It 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: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 75 times \| Downloaded: 34 times Tags (13): async \| asynchronous services \| BLAST \| blastp \| database \| ebi \| example \| looping \| ncbi \| ncbi blast \| protein sequence \| sequence \| uniprot	View Download (v1)
Taverna 2 Original Uploader Katy Wolstencroft	EBI_InterproScan_NewServices (v2) Created: 17/01/11 @ 16:08:48 \| Last updated: 17/01/11 @ 16:12:40 Credits: Katy Wolstencroft Hamish McWilliam Stian Soiland-Reyes Attributions: EBI_InterProScan for Taverna 2 EBI_InterProScan for Taverna 2 EBI_InterProScan License: Creative Commons Attribution-Share Alike 3.0 Unported License 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: 62 times \| Downloaded: 42 times Tags (11): async \| asynchronous services \| ebi \| example \| interpro \| interproscan \| looping \| protein domain \| protein family \| protein motif \| protein sequence	View Download (v2)
Taverna 2 Original Uploader Katy Wolstencroft	EMBL-EBI ClustalW2_SOAP (v1) Created: 17/01/11 @ 16:48:40 \| Last updated: 17/01/11 @ 16:48:37 Credits: Katy Wolstencroft Hamish McWilliam Attributions: EMBL-EBI ClustalW2 (SOAP) EBI_ClustalW2 License: Creative Commons Attribution-Share Alike 3.0 Unported License Perform a ClustalW2 alignment using the EMBL-EBI’s ClustalW2 (SOAP) service (see http://www.ebi.ac.uk/Tools/webservices/services/msa/clustalw2_soap). 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. Perform a ClustalW2 alignment using the EMBL-EBI’s C... Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 26 times \| Downloaded: 15 times Tags (9): alignment \| async \| asynchronous services \| clustalw \| DNA \| ebi \| looping \| multiple sequence alignment \| protein	View Download (v1)
Taverna 2 Original Uploader Kalai	Generate Atom Signatures of molecules given SDF as input (v1) Created: 13/05/11 @ 17:14:06 \| Last updated: 13/05/11 @ 19:47:24 Credits: Kalai License: Creative Commons Attribution-Share Alike 3.0 Unported License Reference: Natural Product-likeness Score and Its Application for Prioritization of Compound Libraries Peter Ertl,* Silvio Roggo, and Ansgar Schuffenhauer Novartis Institutes for BioMedical Research, CH-4002 Basel, Switzerland http://peter-ertl.com/reprints/Ertl-JCIM-48-68-2008.pdf The natural product likeness scorer implemented by Peter Ertl was originally devised to screen large compound libraries for natural product likeness in drug designing studies. His work is re... Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 46 times \| Downloaded: 19 times Tags (22): bioinformatics \| cdk \| cdk-taverna \| chemoinformatics \| compound \| curation \| drug \| ebi \| example \| filter \| filtering \| metabolism \| metabolite-likeness \| metabolomics \| natural \| open science \| open source \| re-use \| synthetic \| taverna 2 \| workflow \| workflows	View Download (v1)
Taverna 2 Original Uploader Kalai	Scoring small molecules for metabolite likeness/ Natural product likeness (v2) Created: 13/05/11 @ 17:22:28 \| Last updated: 18/03/12 @ 16:41:39 Credits: Kalai License: Creative Commons Attribution-Share Alike 3.0 Unported License Prerequisite: - CDK -Taverna Plugin 0.5.1 http://www.ts-concepts.de/cdk-taverna2/plugin/ - To run this workflow the atom_signatures file of Natural product(NP), Synthetic Molecules(SM) and query structures are needed - This could be generated from GenerateAtomSignatures.t2flow http://www.myexperiment.org/workflows/2120/download?version=1 Description of input ports : NP_file: needs precomputed Atom_signatures of desired Natural product structu... Rating: 0.0 / 5 (0 ratings) \| Versions: 2 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 66 times \| Downloaded: 16 times Tags (22): bioinformatics \| cdk \| cdk-taverna \| chemoinformatics \| compound \| curation \| drug \| ebi \| example \| filter \| filtering \| metabolism \| metabolite-likeness \| metabolomics \| natural \| open science \| open source \| re-use \| structure \| synthetic \| workflow \| workflows	View Download (v2)
Taverna 2 Original Uploader Kalai	Plotting distribution of natural product likeness scores (v1) Created: 13/05/11 @ 17:34:58 \| Last updated: 13/05/11 @ 17:35:08 Credits: Kalai License: Creative Commons Attribution-Share Alike 3.0 Unported License Prerequisite: CDK -Taverna Plugin 0.5.1 http://www.ts-concepts.de/cdk-taverna2/plugin/ - To run this workflow you need a Score file which is written to text file. - This could be generated from ScorerActivity.t2flow http://www.myexperiment.org/workflows/2121/download?version=1 Description of input ports : score_file: Path to file name that has pre computed scores. Note: While passing file as input it could be passed as list of many files or single fi... Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 31 times \| Downloaded: 13 times Tags (24): bioinformatics \| cdk \| cdk-taverna \| chemoinformatics \| compound \| curation \| drug \| ebi \| example \| filter \| filtering \| metabolism \| metabolite-likeness \| metabolomics \| natural \| open science \| open source \| plot \| re-use \| structure \| synthetic \| taverna2 \| workflow \| workflows	View Download (v1)
Taverna 2 Original Uploader Rafael C. Jimenez	EBI PICR, find cross-references for protein accessions (v2) Created: 18/05/11 @ 09:36:26 \| Last updated: 29/05/11 @ 17:35:20 Credits: Rafael C. Jimenez License: Creative Commons Attribution-Share Alike 3.0 Unported License Find cross-references (based on 100% sequence identity) for protein accessions from more than 95 distinct databases. For instance input a list of IPI accessions and find cross-references for Swissprot and Ensembl. Mappings can be limited by source database, taxonomic ID and activity status. Rating: 0.0 / 5 (0 ratings) \| Versions: 2 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 10 times \| Downloaded: 9 times Tags (5): cross-references \| ebi \| mapping \| picr \| protein accessions	View Download (v2)
Taverna 2 Original Uploader Rafael C. Jimenez	Find Biological Models by GO. (v1) Created: 29/05/11 @ 21:44:22 \| Last updated: 29/05/11 @ 21:44:23 Credits: Rafael C. Jimenez License: Creative Commons Attribution-Share Alike 3.0 Unported License Find Biological Models (Ids and Names) from Biomodels querying by Gene Ontology terms. Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 12 times \| Downloaded: 7 times Tags (2): biomodels \| ebi	View Download (v1)
Taverna 2 Original Uploader Rafael C. Jimenez	Find Reactome pathways and reactions by GO (v1) Created: 29/05/11 @ 19:09:23 \| Last updated: 29/05/11 @ 19:09:25 Credits: Rafael C. Jimenez License: Creative Commons Attribution-Share Alike 3.0 Unported License Find Reactome pathways and reactions (names and accessions) in Human querying by a Gene Ontology term. This is an example of how to use the Reactome Biomart service in Taverna. Many other possibilities are possible by modifying the filters and attributes options of the service. Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 12 times \| Downloaded: 7 times Tags (5): biomart \| ebi \| pathway \| reaction \| reactome	View Download (v1)
Taverna 2 Original Uploader Rafael C. Jimenez	Find PRIDE experiments by GO (v1) Created: 29/05/11 @ 19:07:59 \| Last updated: 29/05/11 @ 19:08:01 Credits: Rafael C. Jimenez License: Creative Commons Attribution-Share Alike 3.0 Unported License Find PRIDE experiments in Human with related information like Cell Type and Tissue location filtering results by Gene Ontology terms. This is an example of how to use the PRIDE Biomart service in Taverna. Many other options are possible by modifying the filters and attributes of this service. Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 6 times \| Downloaded: 7 times Tags (4): biomart \| ebi \| pride \| protein identifications	View Download (v1)
Taverna 2 Original Uploader Rafael C. Jimenez	Molecular Interactions from IntAct PSICQUIC service (REST) (v2) Created: 29/05/11 @ 01:32:18 \| Last updated: 05/10/11 @ 00:20:00 Credits: Rafael C. Jimenez License: Creative Commons Attribution-Share Alike 3.0 Unported License Get molecular interaction data in psi-mitab25 from IntAct through its REST PSICQUIC service. As input you can use an Uniprot Acc like "P99999" or a MIQL query like "alias:KHDRBS1". Rating: 0.0 / 5 (0 ratings) \| Versions: 2 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 8 times \| Downloaded: 8 times Tags (5): ebi \| intact \| molecular interactions \| protein interaction \| psicquic	View Download (v2)
Taverna 2 Original Uploader Rafael C. Jimenez	Molecular Interactions from IntAct PSICQUIC service (SOAP) (v2) Created: 17/05/11 @ 07:09:30 \| Last updated: 20/07/11 @ 15:14:56 Credits: Rafael C. Jimenez License: Creative Commons Attribution-Share Alike 3.0 Unported License Get molecular interaction data in psi-mitab25 from IntAct through its PSICQUIC service. As input you can use an Uniprot Acc like "P99999" or a MIQL query like "alias:(KHDRBS1 OR HCK)". This workflow finds by itself how many queries needs to make (SOAP service limited to 200 binary interactions per call) to be able to return all the results in one file. Rating: 0.0 / 5 (0 ratings) \| Versions: 2 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 13 times \| Downloaded: 5 times Tags (4): ebi \| intact \| molecular interactions \| psicquic	View Download (v2)
Taverna 2 Original Uploader Rafael C. Jimenez	EBI NCBI BLAST Multi FASTA (v2) Created: 16/07/11 @ 19:08:38 \| Last updated: 16/07/11 @ 19:35:11 Credits: Rafael C. Jimenez License: Creative Commons Attribution-Share Alike 3.0 Unported License This workflow performs multiple sequence similarity searches using the NCBI blast at the EBI. It 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. If you want to make a blast search for more than 10 sequences I would recommend you to run the workflow using the comm... Rating: 0.0 / 5 (0 ratings) \| Versions: 2 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 25 times \| Downloaded: 17 times Tags (6): BLAST \| ebi \| FASTA \| fasta format \| sequence \| similarity	View Download (v2)

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Creator:

Hamish McWilliam

EBI Web Services

Created: 11/07/08 @ 01:24:33 | Last updated: 11/07/08 @ 01:43:30

The European Bioinformatics Institiute offers a wide range of services covering may biological anfd bioinformatics domains. This Pack col.lates a set of workflows that provide wrappers for web services developed, and maintained by the EBI.

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Creator:

Kalai

Natural product likeness filter

Created: 13/05/11 @ 19:35:39 | Last updated: 29/08/11 @ 14:25:47

Reference: Natural Product-likeness Score and Its Application for Prioritization of Compound Libraries Peter Ertl,* Silvio Roggo, and Ansgar Schuffenhauer Novartis Institutes for BioMedical Research, CH-4002 Basel, Switzerland http://peter-ertl.com/reprints/Ertl-JCIM-48-68-2008.pdf The natural product likeness scorer implemented by Peter Ertl was originally devised to screen large compound libraries for natural product likeness in drug designing studies. His work...

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