Workflows

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Showing 19 results. Use the filters on the left and the search box below to refine the results.
Type: Taverna 1 Tag: protein User: Hamish McWilliam Licence: by

Workflow Nucleotide_InterProScan (4)

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Note: the WSInterProScan web service used by this workflow is no longer available haveing been replaced by the EMBL-EBI's InterProScan (REST) (http://www.ebi.ac.uk/Tools/webservices/services/pfa/iprscan_rest) and InterProScan (SOAP) (http://www.ebi.ac.uk/Tools/webservices/services/pfa/iprscan_soap) web services. Thus the workflow described here no longer works, see the alternative workflows for the InterProScan (SOAP) service for workflows which use the new services. Run InterProScan using a...

Created: 2008-10-26 | Last updated: 2011-04-01

Credits: User Hamish McWilliam

Attributions: Workflow EBI_InterProScan Workflow EBI_NCBI_BLAST Workflow Nucleotide_ORF_translation Workflow Fasta_string_to_fasta_list Workflow Sequence_or_ID

Workflow EBI_Blast2InterPro (2)

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Note: the WSInterProScan web service used by this workflow is no longer available haveing been replaced by the EMBL-EBI's InterProScan (REST) (http://www.ebi.ac.uk/Tools/webservices/services/pfa/iprscan_rest) and InterProScan (SOAP) (http://www.ebi.ac.uk/Tools/webservices/services/pfa/iprscan_soap) web services. Thus the workflow described here no longer works, see the alternative workflows for the InterProScan (SOAP) service for workflows which use the new services. Perform a BLAST search a...

Created: 2008-10-26 | Last updated: 2012-08-22

Credits: User Hamish McWilliam

Attributions: Workflow EBI_WU-BLAST Workflow EBI_dbfetch_fetchBatch Workflow Fasta_string_to_fasta_list Workflow EBI_InterProScan

Workflow Protein_search_fetch_align_tree (2)

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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

Credits: User Hamish McWilliam

Attributions: Workflow EBI_ClustalW2 Workflow EBI_ClustalW2_phylogentic_tree Workflow EBI_dbfetch_fetchBatch Workflow EBI_WU-BLAST

Workflow Protein_transmembrane_prediction (2)

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Note: the WSInterProScan web service used by this workflow is no longer available haveing been replaced by the EMBL-EBI's InterProScan (REST) (http://www.ebi.ac.uk/Tools/webservices/services/pfa/iprscan_rest) and InterProScan (SOAP) (http://www.ebi.ac.uk/Tools/webservices/services/pfa/iprscan_soap) web services. Thus the workflow described here no longer works, see the alternative workflows for the InterProScan (SOAP) service for workflows which use the new services. Transmembrane and signal...

Created: 2008-10-26 | Last updated: 2011-04-01

Credits: User Hamish McWilliam

Attributions: Workflow EBI_InterProScan_tmhmm_signalp Workflow EBI_Phobius Workflow tmap_single_sequence

Workflow EBI_InterProScan_tmhmm_signalp (4)

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Note: the WSInterProScan web service used by this workflow is no longer available haveing been replaced by the EMBL-EBI's InterProScan (REST) (http://www.ebi.ac.uk/Tools/webservices/services/pfa/iprscan_rest) and InterProScan (SOAP) (http://www.ebi.ac.uk/Tools/webservices/services/pfa/iprscan_soap) web services. Thus the workflow described here no longer works, see the alternative workflows for the InterProScan (SOAP) service for workflows which use the new services. Use the TMHMM and Signal...

Created: 2008-10-26 | Last updated: 2011-04-01

Credits: User Hamish McWilliam

Attributions: Workflow EBI_InterProScan

Workflow EBI_PICR_Sequence_to_UniParc_and_InterPro (2)

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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 s...

Created: 2008-06-08 | Last updated: 2008-06-08

Credits: User Hamish McWilliam

Attributions: Workflow EBI_dbfetch_UniParc Workflow EBI_Fetch_InterPro_Matches_UniParc Workflow EBI_PICR_Sequence_to_ID

Workflow tmap_single_sequence (2)

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Simple workflow using tmap to find transmembrane regions, using a single sequence as input.

Created: 2008-06-01 | Last updated: 2008-06-02

Credits: User Hamish McWilliam

Attributions: Workflow Sequence_or_ID

Workflow 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: User Hamish McWilliam

Attributions: Workflow EBI_FASTA Workflow EBI_ClustalW2 Workflow EBI_dbfetch_fetchBatch

Workflow EBI_Phobius (2)

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The Phobius tool predicts transmembrane domains and signal peptide region from a protein sequence. This workflow uses the EBI's WSPhobius web service (see http://www.ebi.ac.uk/Tools/webservices/services/phobius) to access the tool. The predicted features are returned in a UniProtKB style feature listing.

Created: 2008-06-01 | Last updated: 2008-06-02

Credits: User Hamish McWilliam

Workflow Structure_or_ID (1)

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Given a structure or structure entry identifer (e.g. PDB:1crn), return the structure in PDB format. If a structure identifier, in database:identifier format, is input the EBI's WSDbfetch web service (see http://www.ebi.ac.uk/Tools/webservices/services/dbfetch) is used to retrive the structure in PDB format. Otherwise the input is assumed to be a formated structure and is passed through to the output.

Created: 2008-06-06

Credits: User Hamish McWilliam

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