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Showing 45 results. Use the filters on the left and the search box below to refine the results.
Category: Workflow Type: Taverna 1 Tag: protein

Workflow EBI_IntAct (1)

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Find protein binary interactions using the EBI's IntAct service. See http://www.ebi.ac.uk/intact/ for further details.

Created: 2008-07-09

Credits: User Hamish McWilliam

Workflow EBI_DaliLite (1)

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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.

Created: 2008-06-07

Credits: User Hamish McWilliam

Workflow EBI_MPsrch (1)

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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.  

Created: 2008-06-02 | Last updated: 2010-12-06

Credits: User Hamish McWilliam

Workflow blastp using the MRS system (1)

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This blastp workflow uses the blast service of MRS (http://mrs.cmbi.ru.nl). Inputs are a sequence (only amino acids, not a fasta sequence) and a database name. Valid database names that can be used are "sprot", "uniprot", "trembl", "pdb", "refseq", "ipi" and "gpcrdb". Output is returned in XML.

Created: 2008-11-28 | Last updated: 2008-11-28

Credits: User Bas Vroling

Workflow EBI_ScanPS (1)

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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.  

Created: 2008-06-03 | Last updated: 2010-12-06

Credits: User Hamish McWilliam

Workflow M_Fetch_e-T_phylo_boot - (BETA) (1)

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This workflow performs a generic protein sequence analysis. In order to do that a novel protein sequence enters into the software along with a list of known protein identifiers chosen by the biologist to perform a homology search, followed by a multiple sequence alignment and finally a phylogenetic analysis.

Created: 2010-03-10 | Last updated: 2010-03-10

Credits: User Achille Zappa User Hamish McWilliam

Workflow Pfam Based Ortholog Filter (1)

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This workflow filters an Ondex graph based on the occurrence of Pfam orthologs within the graph. The result is a new Ondex graph. The parameters that can be used with this service are as follows: graphId - the ID of the input Graph. outputGraphId - the ID of the output Graph (Optional). If no output graph is specified filtered items will be removed from the input graph. ConfidenceThreshold - Threshold value for inparanoid confidence. Default value is 100. AnnotationScoreThreshold - Threshold...

Created: 2009-08-19

Credits: User Paul Fisher

Workflow Tab Parser (1)

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This workflow takes in a tab separated file, and then parses specific rows and columns from the file into an Ondex Graph. Additional prarameters are provided, though these are optional: graphId Long the ID of the Graph (REQUIRED) input String the plugin input (REQUIRED) skip Integer How many rows to skip at begin of document (Optional). Default value is 22. fromCol Integer Index of concept parser id for from concept. Default value is 0. (REQUIRED) toCol Integer Index of concept par...

Created: 2009-08-19

Credits: User Paul Fisher

Workflow InterProScan (SOAP) (1)

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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.

Created: 2010-12-03 | Last updated: 2013-03-28

Credits: User Hamish McWilliam

Attributions: Workflow EBI_InterProScan Workflow InterProScan (SOAP)

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Workflow retrieve protein sequence and do a BLAST f... (1)

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retrieve protein sequence and do a BLAST from DDBJ Web services   informations on Web services available at http://xml.nig.ac.jp/index.html example accession : Q9NRA8 database : UNIPROT program : blastp  

Created: 2010-09-01 | Last updated: 2010-09-01

Credits: User Lebreton

Attributions: Workflow retrieve protein sequence and do a BLAST and extract position from DDBJ Web services

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