User: Morgan Taschuk

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Drug Target FASTA

Created: 2011-03-30 10:51:26 | Last updated: 2011-04-01 13:10:05

Credits: Morgan Taschuk Andrewsmeaton

Attributions: Compile Protein FASTA from Target to Drug file

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: Plain text

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Parsed UniProt to PubMed (1)

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Uses the parsed Uniprot results (see workflow http://www.myexperiment.org/workflows/26.html) to retrieve information from PubMed.

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

Credits: Morgan Taschuk

Use UniProt to retrieve InterPro data (1)

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Used parsed Uniprot results (see workflowUsed parsed Uniprot results (see workflow http://www.myexperiment.org/workflows/26.html) to retrieve results about the protein from InterPro.

Created: 2011-04-01

Credits: Morgan Taschuk

UniProt to Gene Ontology (1)

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Used parsed Uniprot results (see workflow http://www.myexperiment.org/workflows/26.html) to retrieve results about the protein from Gene Ontology and outputs it in text format.

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

Credits: Morgan Taschuk

Vaccine Targets Workflow (3)

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Comparison of the genome of Bacillus anthracis to closely related strains will allow the discovery of proteins which may be involved in pathogenicity. Based on the biochemical pathways where the protein interacts, vaccines can be designed for these unique proteins. By gaining insight into the biochemical pathways that the unique proteins are involved in, the proteins can also be assessed for potential quality as vaccines. The key components of the vaccine finding system are the following: T...

Created: 2011-03-30 | Last updated: 2011-04-01

Credits: Morgan Taschuk A Team

Print Protein Information to HTML (1)

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Takes in a lot of parameters in order to construct an HTML table to display the information.

Created: 2011-04-01

Credits: Morgan Taschuk

Compile Protein FASTA from Target to Drug ... (1)

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Uses a tab-delimited file with protein target and drug information (created in Ondex) to compile a protein FASTA file including each target.

Created: 2011-03-30 | Last updated: 2011-03-30

Credits: Morgan Taschuk Andrewsmeaton

Print Analysis Information to HTML (2)

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Takes in a lot of parameters in order to construct an HTML header to display the information.

Created: 2011-03-29 | Last updated: 2011-04-01

Credits: Morgan Taschuk

KEGG Pathways and Additional Information f... (2)

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Takes in a tab-delimited BLAST file and finds additional information about the target proteins from KEGG, Gene Ontology, Interpro and PubMed.

Created: 2011-03-29 | Last updated: 2011-03-30

Credits: Morgan Taschuk

Attributions: extract_uniprot_embl_gi.xml

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