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EBI_dbfetch_fetchBatch

Workflow Entry: EBI_dbfetch_fetchBatch

Created at: 31/05/08 @ 20:59:46

Version 1 (of 1)

Version created on: 31/05/08 @ 20:59:46 by: Hamish McWilliam

Title: EBI_dbfetch_fetchBatch

Type: Taverna 1

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Description

From a list of sequence entry identifiers and a database name, fetch the sequences in fasta format using EBI's WSDbfetch service (see http://www.ebi.ac.uk/Tools/webservices/wsdl/WSDbfetch.wsdl).

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Workflow Components

Inputs (2)

Name	Description
ID_list	List of entry identifers from a specific database.
Database	Name of the database to which the identifiers belong. For example "uniprot".

Processors (2)

Name	Type	Description
fetchBatch	arbitrarywsdl	Get a set of database entries (see http://www.ebi.ac.uk/Tools/webservices/services/dbfetch#fetchbatch_db_ids_format_style) See the Service entry for this web service.
Format_list_for_dbfetch	local	Reformat the list of identifiers into a comma-delimited string for use with fetchBatch.

Beanshells (0)

Outputs (1)

Name	Description
Sequences	Set of sequences in fasta format.

Links (4)

Source	Sink
Database	fetchBatch:db
ID_list	Format_list_for_dbfetch:stringlist
Format_list_for_dbfetch:concatenated	fetchBatch:ids
fetchBatch:fetchBatchReturn	Sequences

Coordinations (0)

Information Workflow Type

Taverna 1

Information Original Uploader

Hamish McWilliam

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Information Credits (1)

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Hamish McWilliam

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Information Statistics

1383 viewings

1114 downloads

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Citations (0)

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Version History

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EBI_dbfetch_fetchBatch

Created by Hamish McWilliam on Saturday 31 May 2008 @ 20:59:46 (UTC)

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Created: 07/04/09 @ 20:13:19

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License: Creative Commons Attribution 3.0 Unported License

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Rating: 0.0 / 5 (0 ratings) | Versions: 2 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 482 times | Downloaded: 177 times

Tags (15):

Taverna 1

Original Uploader

Hamish McWilliam

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Protein_alignment_transmembrane (1)

Created: 01/06/08 @ 12:20:29

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Attributions: EBI_FASTA EBI_ClustalW2 EBI_dbfetch_fetchBatch

License: Creative Commons Attribution 3.0 Unported License

Transmembrane domain prediction using EMBOSS tmap with an input sequence alignment of homolouges: Sequence similarity search (SSS) to find homologues Fetch sequences of hits Multiple sequence alignment (MSA) of hit sequences EMBOSS tmap with alignment from 3. Uses the EBI web services: WSFasta (see http://www.ebi.ac.uk/Tools/webservices/services/fasta) WSDbfetch (see http://www.ebi.ac.uk/Tools/webservices/services/dbfetch) WSClustalW2 (see http://www.ebi.ac.uk/Tools/webservices/servic...