Workflows

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Showing 157 results. Use the filters on the left and the search box below to refine the results.
Type: Taverna 1 Licence: by

Workflow Fasta_string_to_fasta_list (1)

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Split a string containing a set of sequences in fasta format into a list for fasta formated sequences.

Created: 2008-06-06

Credits: User Hamish McWilliam

Workflow EBI_FASTA (1)

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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.  

Created: 2008-05-30 | Last updated: 2010-12-06

Credits: User Hamish McWilliam

Workflow REST access of xml.nig.ac.jp (WABI) (1)

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This workflow has a beanshell script for composing the REST URL for the services at xml.nig.ac.jp  (WABI) This URL is passed to the local worker Get_web_page_from_URL that fetches the requested data. Note: This is a proof of concept of accessing REST services through Taverna. All of WABI's services can more easily be browsed and used in Taverna by adding their WSDL, for instance http://xml.nig.ac.jp/wsdl/GetEntry.wsdl The example invokes the getDDBJEntry(accession) method of the getE...

Created: 2008-10-14 | Last updated: 2008-10-14

Credits: User Stian Soiland-Reyes

Workflow Sequence_or_ID_or_GI (1)

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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.

Created: 2008-06-07

Credits: User Hamish McWilliam

Attributions: Workflow Structure_or_ID

Workflow Structure_or_ID (1)

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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.

Created: 2008-06-06

Credits: User Hamish McWilliam

Workflow EBI_MaxSprout (2)

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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.

Created: 2008-06-05 | Last updated: 2008-06-06

Credits: User Hamish McWilliam

Attributions: Workflow Structure_or_ID

Workflow EBI_InterProScan_with_prompts (1)

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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...

Created: 2008-05-31 | Last updated: 2011-04-01

Credits: User Hamish McWilliam

Attributions: Workflow EBI_InterProScan

Workflow EBI_Fetch_InterPro_Matches_UniParc (1)

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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).

Created: 2008-06-08

Credits: User Hamish McWilliam

Workflow tRNAscan (1)

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Search a nucleotide sequence for tRNA genes using the tRNAscan-SE tool (see http://wiki.bioinformatics.org/TRNAscan-SE). This workflow uses the tRNAscan service at VBI PathPort (see http://pathport.vbi.vt.edu/services/#predict_7).

Created: 2008-06-28

Credits: User Hamish McWilliam

Attributions: Workflow Sequence_or_ID_or_GI

Workflow EBI_CENSOR (2)

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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.

Created: 2008-06-17 | Last updated: 2008-06-25

Credits: User Hamish McWilliam

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