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Type: Taverna 2

Tag: FASTA

Licence: by-sa

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Taverna 2

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Ian Laycock

Compare genome, extract proteins which are... (1)

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Takes GI number for source (non-pathogenic) and target (pathogneic) genomes, extracts list of all proteins from each genome using GenBank database. Outputs prtoeins in FastA format. Creates database from source proteins using formatdb (locally installed) and blasts (local installed) proteins from target against this database. Extracts protens which are unique (no blast hits) to the target (pathogenic) genome based on eValue set by user. Takes unique proteins from target and blasts aga...

Created: 2010-03-19 | Last updated: 2010-03-19

Credits: Ian Laycock nclteamc

Attributions: fetchEnsemblSeqsAndBlast NCBI Gi to Kegg Pathways color_pathway_by_objects

Taverna 2

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Mventosa

Ex (1)

Ex of exercise

Created: 2009-11-16

Credits: Mventosa

Attributions: EBI_InterProScan for Taverna 2

Taverna 2

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Ruben

Example 3 (1)

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Search in the Datenbank SWISS the Sequence 1220173

Created: 2009-10-20

Credits: Ruben

Taverna 2

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Ian Laycock

Retrieve Genome Seqn using gi nos (1)

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Retrieves the genome seqn for both the target and source strains using gi nos

Created: 2010-03-19

Credits: Ian Laycock nclteamc

Taverna 2

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Aurora Cain

All-vs-All blastP commands (1)

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Creates all the necessary command-line commands to execute all-vs-all blastP from the given FASTA files. Includes making the necessary database. Does not execute the commands. For OSX and UNIX/Linux only (due to path separator).

Created: 2015-04-17

Credits: Aurora Cain

Taverna 2

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Stian Soiland-Reyes

Example dbfetch (2)

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Run EBI's dbfetch

Created: 2014-09-03 | Last updated: 2014-09-03

Credits: Stian Soiland-Reyes Katy Wolstencroft

Attributions:

Taverna 2

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Aleksandra Pawlik

Visualize PAV provenance as SVG (1)

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VoID descriptions are fetched as Turtle, cleaned up to be valid OWL ontology and include useful labels, processed through the OWL reasoner Pellet; this adds inferred PROV statements to the RDF, which is then fed to the PROV Toolbox, generating an SVG visualization of the provenance. Note that this workflow downloads CWM, Pellet and ProvToolbox on demand, and uses UNIX command line tools like wget and md5 which are unlikely to work in Windows. This workflow has been tested on Ubuntu 12.10 wit...