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Items tagged with "clustalw" (11)

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Workflows (11)

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_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	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	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 Aailyso	Identify_strain_and_phylogenetic_tree (v1) Created: 20/03/09 @ 15:20:36 \| Last updated: 20/03/09 @ 15:22:25 Credits: Aailyso Hamish McWilliam AID 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: 169 times \| Downloaded: 46 times Tags (6): BLAST \| blast; clustalw \| clustalw \| database \| phylogenetic tree; \| protein	View Download (v1)
Taverna 2 Original Uploader Katy Wolstencroft	BioMart and Emboss Analysis (T2) (v1) Created: 15/09/09 @ 15:05:11 Credits: Katy Wolstencroft Alan Williams Attributions: BiomartAndEMBOSSAnalysis License: Creative Commons Attribution-Share Alike 3.0 Unported License This is the Taverna 2 version of the Biomart and Emboss Analysis workflow http://www.myexperiment.org/workflows/158 Using Biomart and EMBOSS soaplab services, This workflow retrieves a number of sequences from 3 species: mouse, human, rat; align them, and returns a plot of the alignment result. Corresponding sequence ids are also returned. Previous versions of this workflow only returned sequences with an ID mapped to a MIM_morbid_accession. This was primarily to reduce the numbe... Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 292 times \| Downloaded: 85 times Tags (5): alignment \| biomart \| clustalw \| emboss \| homology	View Download (v1)
Taverna 1 Original Uploader Achille Zappa	MY_Multi_Alignment_Phylo (v1) Created: 03/11/09 @ 14:46:38 Credits: Achille Zappa License: Creative Commons Attribution-Share Alike 3.0 Unported License This workflow performs a 'multiple' multiple sequence alignment and phylogenetic analysis. Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 137 times \| Downloaded: 37 times Tags (7): clustalw \| ml \| multiple alignment \| muscle \| nj \| phylogenetic tree \| upgma	View Download (v1)
Taverna 2 Original Uploader wabi	BLAST-ClustalW workflow (v1) Created: 13/05/10 @ 02:11:12 \| Last updated: 13/05/10 @ 02:12:28 Credits: wabi License: Creative Commons Attribution-Share Alike 3.0 Unported License Execute blastn against DDBJ database with a given DNA sequence and compare the alignment regions of high similar sequences by using ClustalW. Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 49 times \| Downloaded: 30 times Tags (4): 16s ribosomal rna \| BLAST \| clustalw \| ddbj	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	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)