EBI_dbfetch_UniParc

Created: 2008-06-08 14:05:40

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From a list of UniParc entry identifers get the complete entries using the EBI's WSDbfetch service (see http://www.ebi.ac.uk/Tools/webservices/services/dbfetch).

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Workflow Components

Inputs (1)

Name	Description
ID_list	List of UniParc identifiers (e.g. UPI0000000001).

Processors (3)

Name	Type	Description
Extract_entries	local	Extract the UniParc entries from the XML document.
Format_list_for_dbfetch	local	Convert list of identifers into a comma-delimited string for use with fetchBatch.
fetchBatch	arbitrarywsdl	Get a set of database entries (see http://www.ebi.ac.uk/Tools/webservices/services/dbfetch#fetchbatch_db_ids_format_style)

Beanshells (0)

Outputs (2)

Name	Description
UniParc_entries	The set of UniParc entries as a single XML document.
UniParc_entries_list	A list of UniParc entries in XML format.

Links (5)

Source	Sink
Format_list_for_dbfetch:concatenated	fetchBatch:ids
ID_list	Format_list_for_dbfetch:stringlist
fetchBatch:fetchBatchReturn	Extract_entries:xml-text
Extract_entries:nodelistAsXML	UniParc_entries_list
fetchBatch:fetchBatchReturn	UniParc_entries

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Taverna 1

Information Uploader

Hamish McWilliam

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Hamish McWilliam

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Information Attributed By (1)

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EBI_PICR_Sequence_to_UniParc_and_InterPro

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2464 viewings

2272 downloads

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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).

Created: 2008-05-31

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An implmentation of the classical sequence analysis workflow: Find homologues (sequence similarity search) Fetch homologues Align homologues (multiple sequence alignment) Produce phylogenetic tree In this implementation the EBI webservices are used: WU-BLAST (WSWUBlast) blastp vs. UniProtKB dbfetch (WSDbfetch) ClustalW (WSClustalW2) ClustalW (WSClustalW2) Note: this version does not add the inital query sequence to the alignment, and so is most useful when used with the identifers...

Created: 2009-04-07

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Attributions: EBI_ClustalW2 EBI_ClustalW2_phylogentic_tree EBI_dbfetch_fetchBatch EBI_WU-BLAST