EBI_PICR_Sequence_to_UniParc_and_InterPro

Created: 2008-06-08 13:53:39 Last updated: 2008-06-08 14:10:02

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Given a protein sequence get some information about it:

Does this protein sequence occur in any of the protein databases (e.g. UniProtKB, PDB, etc.). Using the PICR web service (see http://www.ebi.ac.uk/Tools/picr/) map the sequence to a UniParc identifer.
Which entries in the protein databases have this sequence. Using the UniParc database (see http://www.ebi.ac.uk/uniprot/database/DBDescription.html#uniparc) a summary of the databases and the entries in those databases which have this sequence is obtained.

3. Does any protein domain or family information exist for this sequence. Using the InterPro Matches UniParc database (see http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-page+LibInfo+-lib+IPRMC_UNIPARC) a summary of the known signature matches is obtained.

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Workflow Components

Inputs (1)

Name	Description
Sequence	Input protein sequence in fasta format.

Processors (4)

Name	Type	Description
Spit_PICR_result	local
EBI_dbfetch_UniParc	workflow
EBI_Fetch_InterPro_Matches_UniParc	workflow
EBI_PICR_sequence_to_ID	workflow

Beanshells (2)

Name	Description	Inputs	Outputs
Build_InterPro_Matches_UniParc_URL	Construct SRS@EBI URL to get the InterPro matches UniParc (IPRMC_UNIPARC) entry.	uniparc_id	iprmc_uniparc_url
Check_for_SRS_error	Check the data returned by SRS for errors, and "not found" messages. In this case a simple check for HTML tags.	input	output

Outputs (3)

Name	Description
PICR_result	Result from the PICR service. Contains a mapping to the UniParc identifer (UPI) and to various other protein databases based on the UniParc data.
UniParc_entry	Entry from UniParc corresponding to the input sequence.
InterPro_matches	InterPro Matches UniParc entry corresponding to the input sequence.

Links (7)

Source	Sink
Sequence	EBI_PICR_sequence_to_ID:Sequence
EBI_PICR_sequence_to_ID:PICR_result	Spit_PICR_result:input
EBI_Fetch_InterPro_Matches_UniParc:InterPro_Matches	InterPro_matches
EBI_PICR_sequence_to_ID:PICR_result	PICR_result
Spit_PICR_result:UPI	EBI_Fetch_InterPro_Matches_UniParc:UniParc_ID
EBI_dbfetch_UniParc:UniParc_entries	UniParc_entry
Spit_PICR_result:UPI	EBI_dbfetch_UniParc:ID_list

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Taverna 1

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Hamish McWilliam

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Hamish McWilliam

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EBI_PICR_Sequence_to_UniParc_and_InterPro

Created by Hamish McWilliam on Sunday 08 June 2008 13:53:39 (UTC)

Last edited by Hamish McWilliam on Sunday 08 June 2008 13:53:40 (UTC)
EBI_PICR_Sequence_to_UniParc_and_InterPro

Created by Hamish McWilliam on Sunday 08 June 2008 13:53:39 (UTC)

Last edited by Hamish McWilliam on Sunday 08 June 2008 14:10:02 (UTC)

Revision comment:

Add processor descriptions.

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Taverna 1

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EBI_dbfetch_UniParc (1)

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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).

Created: 2008-06-08

Credits: Hamish McWilliam

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Protein_alignment_transmembrane (1)

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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...

Created: 2008-06-01

Credits: Hamish McWilliam

Attributions: EBI_FASTA EBI_ClustalW2 EBI_dbfetch_fetchBatch