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DAS sequence retrieval and parsing with JDAS (1)

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Retrieve Protein or Genome sequences using the Distributed Annotation System (DAS) and create your own text output by modifying the JDAS component. To be able to use this workflow with JDAS, copy this file … http://www.ebi.ac.uk/~maven/m2repo/uk/ac/ebi/das/jdas/1.0.3/jdas-1.0.3.jar … to the lib folder inside the Taverna application. This jar file is a dependency needed to parse DAS outputs.

Created: 2011-05-30 | Last updated: 2011-05-30

Credits: Rafael C. Jimenez

DAS sequence retrieval (2)

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Retrieve Protein or Genome sequences using the Distributed Annotation System (DAS).

Created: 2011-05-30 | Last updated: 2011-05-30

Credits: Rafael C. Jimenez

Threshold BLAST results (2)

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Thresholds tab-delimited BLAST results to a certain percent identity.

Created: 2011-03-28 | Last updated: 2011-04-01

Credits: Morgan Taschuk A Team

Drug Re-Purposing Workflow (6)

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The drug repurposing workflow system screens at least 20 bacterial proteomes against this set of proteins that are already being treated against using established drugs. By screening the bacterial proteomes it will be possible to find proteins of highly similar structure to those that are existing drug protein targets and so this will infer that it is highly likely that the drugs can be used as antimicrobials against these proteins of highly similar structure. Proteomes that will be screene...

Created: 2011-03-25 | Last updated: 2011-04-01

Credits: Morgan Taschuk A Team

Extract unique proteins from blast results (4)

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The workflow parses uses the tab-delimited BLAST results to determine the unique proteins found in the target genome that have no similarity to the source genome.The workflow parses uses the blast results to determine the unique proteins found in the target genome that have no similairty to the source genome. Using these unique protein ids, and the original target protein fasta file, a fasta file of unique proteins is created.This workflow allows you to configure a BioMart query to fetch sequ...

Created: 2011-03-24 | Last updated: 2011-04-01

Credits: Morgan Taschuk A Team

Attributions: Parse unique proteins from Blast file

Create custom-made GPCR alignments (1)

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This workflow allows you to create your own GPCR alignments. The alignments are built from the residues that are annotated with the general residue numbers. Alignments are therefore not built using standard alignment algorithms but are created by selecting residues that are likely to share the same position in the three-dimensional structure. Users can select the proteins and residue positions that should be aligned, allowing for the creation of e.g. an alignment of all binding pocket residue...

Created: 2010-08-24 | Last updated: 2010-08-24

Credits: Bas Vroling

BLAST against the GPCRDB (1)

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With this workflow you can submit a BLAST query to the GPCRDB. Input requires a sequence with amino acids only.

Created: 2010-08-24 | Last updated: 2010-08-24

Credits: Bas Vroling

Retrieve a protein from the GPCRDB (1)

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This small workflow illustrates how to use the web service access provided by the GPCRDB in Taverna. The proteinId input field is case sensitive and by default the identifiers in the GPCRDB are lowercase. You can try this mini-workflow with e.a. 'adrb2_human'.

Created: 2010-08-24 | Last updated: 2010-08-24

Credits: Bas Vroling

KEIO Bioinformatics Web Service - a genera... (2)

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This workflow generates a sequence logo image for a set of amino acid sequences of FOXP2 gene, by downloading the amino acid sequences in Fasta format through Togo Web Service with UniProt identifiers (togoWS, provided by the G-language Genome Analysis Environment SOAP Service), running BLAST web service (runBLAST), retrieving a set of sequences from ID list (togoWS), aligning the sequence with MUSCLE (runMUSCLE), extracting a certain region from the alignment (extractalign, provided by Soapl...

Created: 2010-08-13 | Last updated: 2010-11-19

Credits: cory (Kazuki Oshita)