Protein_transmembrane_prediction

Created: 2008-10-26 21:16:10      Last updated: 2011-04-01 08:57:10

Note: the WSInterProScan web service used by this workflow is no longer available haveing been replaced by the EMBL-EBI's InterProScan (REST) (http://www.ebi.ac.uk/Tools/webservices/services/pfa/iprscan_rest) and InterProScan (SOAP)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 peptide prediction using three methods:

  1. EMBOSS tmap with a single sequence. Uses Soaplab tmap.
  2. Phobius. Uses EBI's WSPhobius web service.
  3. TMHMM and SignalP. Uses the TMHMM and SignalP methods of InterProScan via the EBI's WSInterProScan service.

The results of the three methods are converted into GFF format and collated.

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  • Friday 04 July 2008 14:23:52 (UTC)

    Any chance of getting the subworkflows for this as well. Couldn't find them online and I want the polling part. i.e. For loads of the EBI jobs, you have  to write beanshells to check if the job is done. It would nice to see a write up on how to create workflows for this.

    Thanks,

    Niall

  • Tuesday 08 July 2008 17:53:35 (UTC)

    Hi Niall. The subworkflows are included. If you download this workflow, load it into Taverna and navigate to the nexted workflows you can save them indpendantly using the normal save functionality.

    The general process required to poll for service results is explained on the EBI website (see http://www.ebi.ac.uk/Tools/webservices/tutorials/workflow/taverna). In brief it uses Taverna's retry mechanism and a nested workflow which fails if the job has not completed.

     

  • Saturday 01 November 2008 12:14:12 (UTC)

    Great!

    With which proteins have you tried this workflow? Do you have an estimate for its precision/accuracy?

    There are other protein structure preditors that merge results from various sources, and combine them, to obtain a better prediction.
    Is this the same approach you are using in this protocol?
    e.g. I know of this predictor (http://pongo.biocomp.unibo.it/), but it is only for membrane proteins structure. Is it something similar?

    How are the gff results merged at the end of the workflow? What does Gff_output contains, exactly?




Workflow Other workflows that use similar services (34)

Only the first 2 workflows that use similar services are shown. View all workflows that use these services.


Workflow Nucleotide_InterProScan (4)

Thumb
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)

Thumb
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