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Showing 19 results. Use the filters on the left and the search box below to refine the results.
Tag: ebi Licence: by-sa

Workflow Nucleotide InterProScan for the BioExtract... (3)

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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...

Created: 2009-04-16 | Last updated: 2009-07-01

Credits: User Carol Lushbough User Hamish McWilliam

Attributions: Workflow Nucleotide_InterProScan

Workflow Multiple Protein Alignment Profiling(1) (4)

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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.

Created: 2010-01-13 | Last updated: 2010-11-17

Credits: User Carol Lushbough User Alan Williams

Attributions: Workflow A workflow version of the EMBOSS tutorial

Workflow EBI_NCBI_BLAST (4)

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This workflow performs an NCBI blast at the EBI. It accepts a protein sequence as input. Default values have been set for the search database (Uniprot), the number of hits to return (10), and all scoring and matrix options. These can be changed in the workflow by altering the string constant values if required. This workflow uses the new EBI services. They are asynchronous and so require looping over the nested workflow (Status) until the workflow has finished. Many of the EBI services now wo...

Created: 2011-01-17 | Last updated: 2013-05-30

Credits: User Katy Wolstencroft User Hamish McWilliam

Attributions: Workflow EBI_NCBI_BLAST

Workflow Triplify EB-Eye databases list from EBI [m... (1)

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TAG: knowledgescope, eb-eye, bio2rdf, banff_manifesto, rdf, ebi, soap

Created: 2009-11-30 | Last updated: 2009-11-30

Credits: User Francois Belleau

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Workflow Scoring small molecules for metabolite lik... (2)

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 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...

Created: 2011-05-13 | Last updated: 2012-03-18

Credits: User Kalai

Workflow EMBL-EBI ClustalW2_SOAP (2)

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Perform a ClustalW2 alignment of protein sequences 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.

Created: 2011-01-17 | Last updated: 2013-01-30

Credits: User Katy Wolstencroft User Hamish McWilliam

Attributions: Workflow EMBL-EBI ClustalW2 (SOAP) Workflow EBI_ClustalW2

Workflow EBI_InterproScan_NewServices (2)

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This workflow performs an interproscan at the EBI on sequences provided as input. The output is provided as text and xml. 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.

Created: 2014-04-03 | Last updated: 2014-04-09

Credits: User Alex Nenadic

Workflow Blast_Align_and_Tree (2)

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This workflow accepts a protein sequence as input. This sequence is compared to others in the Uniprot database, using the NCBI BLAST Web Service from the EBI (WSDL), and the top 10 hits are returned (Nested workflow:EBI_NCBI_BLast). For each extracted hit, the Uniprot REST service returns the protein sequence in FASTA format. The workflow concatenates the 10 protein sequences and submits them as input to the EBI CLustalw service (Nested workflow EMBL_EBI_clustalw2_SOAP). These sequences are ...

Created: 2013-01-28 | Last updated: 2013-01-30

Credits: User Katy Wolstencroft User Hamish McWilliam

Attributions: Workflow Protein_search_fetch_align_tree

Workflow EBI NCBI BLAST Multi FASTA (2)

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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...

Created: 2011-07-16 | Last updated: 2011-07-16

Credits: User Rafael C. Jimenez

Workflow Find Biological Models by GO. (1)

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Find Biological Models (Ids and Names) from Biomodels querying by Gene Ontology terms.

Created: 2011-05-29 | Last updated: 2011-05-29

Credits: User Rafael C. Jimenez

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