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InviteWorkflow Entry: dbfetch tutorial
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 Version 1
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Version created on:
22/09/08 @ 01:05:36
by:
Steffen Möller
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Last edited on: 22/09/08 @ 01:05:37 by: Steffen Möller
Title: dbfetch tutorial
Type: Taverna 1
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Description
This workflow eases entry in the world of Taverna with one of the key tasks - the retrieval of plain data. The dbfetch offers sequence and structure data from a large variety of sources. A first execution of this workflow informs about these in the "getSupportedDBs" output. Also the formats and styles are listed. The two inputs allow for the specification of a query that leaves the format with "default" (which is different for every database, "native" would be a better fit), the style is always "raw". With the output being presented as a list of strings, which is very slow for larger entries, the list of lines are merged into single strings for each entry prior to the display.
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http://www.myexperiment.org/workflows/397/download?version=1
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[1] - dbfetch tutorial
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Original Uploader |
Created: 07/04/11 @ 22:28:28 | Last updated: 07/04/11 @ 22:39:44
Credits:
License: Creative Commons Attribution-Share Alike 3.0 Unported License
This workflow retrieves a fasta sequence or blast report from an id. Firstly, given some inputs (e.g. ids:EDL10223.1, format:fasta, style:default and db:emblcds), it returns the sequence in fasta format associated to those inputs using the EBI's WSDbfetch web service (see http://www.ebi.ac.uk/Tools/webservices/services/dbfetch).
Next, we obtain a Blast report from this fasta sequence and some others parameters. The final result in that case corresponds with the same fasta sequence introduced...
Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0 Viewed: 22 times | Downloaded: 6 times This Workflow has no tags! |
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Original Uploader |
Created: 03/10/07 @ 18:36:27 License: Creative Commons Attribution-No Derivative Works 3.0 Unported License
Translate Nucleotide sequence into Peptide sequence using EBI Service.
Find nucleotide sequence from EBI wsdbfetch(using ref.seq Id NM_005700)
2. Translation nucleotide sequence(from 1) into peptide sequence using EBI EMBOSS4 transeq.
Rating: 2.0 / 5 (1 rating) | Versions: 2 | Reviews: 0 | Comments: 1 | Citations: 0 Viewed: 202 times | Downloaded: 84 times Tags (4): |
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Non-Information Resource URI: http://www.myexperiment.org/workflows/397
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Copyright © 2007 - 2011 The University of Manchester and University of Southampton
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