Workflows

RDKit-pains (4)

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If you like this workflow, please reference our paper doi:10.1002/minf.201100076, and check the related workflows RDKit-pains-parallel, and Indigo-pains.*** Update 20151119 - using KNIME 3 and RDKit version of PAINS queries ***Implementation of the PAINS filters[1] using the RDKit (3.0.0.201511131320) nodes in KNIME (3.0.1). Original PAINS filters were published in SLN format. This workflow contains the SMARTS form of the filters published by Greg Landrum as part of the RDKit library[2], whic...

Created: 2011-02-07 | Last updated: 2015-11-19

Credits: sauberns

Attributions: Indigo-pains

EBI_PICR_Sequence_to_UniParc_and_InterPro (2)

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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...

Created: 2008-06-08 | Last updated: 2008-06-08

Credits: Hamish McWilliam

Attributions: EBI_dbfetch_UniParc EBI_Fetch_InterPro_Matches_UniParc EBI_PICR_Sequence_to_ID

Fetch today's xkcd comic (1)

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Use the local java plugins and some filtering operations to fetch the comic strip image from http://xkcd.com/ Based on the FetchDailyDilbert workflow.

Created: 2008-03-05 | Last updated: 2008-04-07

Credits: Tomoinn Stian Soiland-Reyes

Attributions:

EBI_NCBI_BLAST (1)

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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...

Created: 2008-05-31 | Last updated: 2010-12-06

Credits: Hamish McWilliam

EBI WU-BLAST with program and database sel... (3)

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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...

Created: 2009-07-04 | Last updated: 2010-12-06

Credits: Hamish McWilliam

Attributions: EBI_WU-BLAST

Retrieve sequence in EMBL format (3)

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This workflow retrieves a sequence associated with its features in embl format

Created: 2009-06-17

Credits: Franck Tanoh Tomoinn Stuart Owen

EBI_ClustalW2_phylogentic_tree (2)

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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).

Created: 2009-04-07

Credits: Hamish McWilliam

Fetch PDB flatfile from RCSB server (1)

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Given an identifier such as '1crn' fetches the PDB format flatfile and returns the corresponding 3D image of the protein.

Created: 2008-03-05 | Last updated: 2008-03-31

Credits: Tomoinn

A workflow version of the EMBOSS tutorial (1)

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Designed to show the use of EMBOSS based Soaplab services from Taverna, this workflow has no inputs as all initial values are specified as string constants. A sequence set is fetched using the seqret tool, then simultaneously scanned for predicted transmembrane regions and subjected to a multiple alignment using emma. This alignment is then plotted to a set of PNG images and also used to build a profile using the prophecy and prophet tools.

Created: 2008-03-05 | Last updated: 2008-03-25

Credits: Tomoinn

tmap_single_sequence (2)

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Simple workflow using tmap to find transmembrane regions, using a single sequence as input.

Created: 2008-06-01 | Last updated: 2008-06-02

Credits: Hamish McWilliam

Attributions: Sequence_or_ID