MkDom2

PASSED
1899
Service version1.0
Contributor URLhttp://prodom.prabi.fr/prodom/current/documentation/mkdom2.html
WSDL URLhttp://prodom.prabi.fr/prodom/current/wsdl/essairunmkdom.wsdlPASSED

MkDom2 is the program used routinely to build each new release of ProDom. The algorithm relies on the assumption that the shortest amino acid sequence corresponds to a single domain, and may be used as a query to screen the database with the psi-blast program, in order to cluster homologous domains. To build ProDom, we run this program on the UniProt (swissprot/trembl) Knowledge Database, but it can be run on any set of protein sequences in a fasta file.

Inputs:

  • a file containing the sequences to analyse in fasta format
  • psi-blast parameters. Default will be -j 10 -e 0.01 -h 0.01. If you want to change something please enter INTER= value to change -j option, E_EXPECT=value for -e option and H_EXPECT=value for -h option.

Outputs:

  • the log file
  • the alignment file of the sequences in srs format
  • the results of the analysis in xdom format
  • the project file used to launch xdom faster

    • A perl script is available here to run this webservice from your computer. Please install SOAP Lite before.

    A description of the WSDL service:

    MkDomService

    Namespace: http://prodom.prabi.fr/mkdom

    • Port: MkDomPort
    • Location: http://prodom.prabi.fr/prodom/2006.1/cgi-bin/essaimkdom.cgi
    • Protocol: http://schemas.xmlsoap.org/soap/http
    • Default Style: document

    Operations

    runMkDom

    Calculate mkdom on fasta data

    • SOAP Action: http://prodom.prabi.fr/mkdom#runMkDom
    • Input Message: MkDomRequestMsg
      • inputWrapper
        • runMkDom type
          • InputFastaSeqs type string
            • ParametersBlast type string
        • Output Message: MkDomResponseMsg
          • outputWrapper
            • runMkDomResponse type
              • output_in_mkdom_format type string
                • log_output type string
                  • alignment_output type string
                    • project_file type string

                WSDL Changes

                DateDescription of Changes
                3rd June 2009First Snapshot
                PASSED

                Test #1: mkdomTest

                This is a test for the MkDom2 webservice. It uses perl and SOAPlite. It includes a test using a short fasta file (7 sequences) as input and checks whether :

                • the output is not empty
                • the first output element is in correct xdom format and contains 7 elements
                • the second output element (the log file) indicates a normal end of the program
                • the third output element is in correct srs format and contains 4 domain families
                • the last output element is a valid url to webdom (domain visualization)
                Submitted by lauranne.duquenne on Tue, 06/02/2009 - 15:01
                »

                blog website list example

                Submitted by elaine on Tue, 05/04/2010 - 12:14.

                3 hours outside chengdu for china travel tips, the capital of Sichuan province, is the Wolong Nature Preserve, the largest panda reserve in China. The center tries to ensure the Giant Panda species can continue to exist. Tourists can observe pandas in their natural habitat and can also help researchers feed and play with these beautiful and threatened animals from china travel tips

                »