MkDom2

By | September 22, 2011

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.

    Name
    MkDom2
    Documentation
    http://prodom.prabi.fr/prodom/current/documentation/mkdom2.html
    Protocol
    SOAP
    WSDL
    Endpoint
    http://prodom.prabi.fr/prodom/2006.1/cgi-bin/essaimkdom.cgi
    Topic
    Domains
    Type
    Analysis
    Tags
    , , , , ,
    Description

    MkDom2 is the program used routinely to build each new release of ProDom. The algorithm relies on the assumption that [...]

    Further information

    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.

    Original source
    BioCatalogue

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