MkDom2 SOAP

Provider:
PRABI – Rhone-Alpes Bioinformatics Center

Location:
France

Submitter / Source:
ProDom team (about 1 year ago)

Base URL:
http://prodom.prabi.fr/prodom/2006.1/cgi-bin/essaimkdom.cgi

WSDL Location:
http://prodom.prabi.fr/prodom/current/wsdl/essairunmkdom.wsdl(download last cached WSDL file)

Documentation URL(s): ProDom team (about 1 year ago)http://prodom.prabi.fr/prodom/current/documentation/mkdom2.html

Login to add a documentation URL Description(s): ProDom team (about 1 year ago)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.

Login to add a description License(s): None Login to add license info Cost: No info yet Login to add cost info Usage Conditions: No info yet Login to add usage conditions info Contact Info: None Login to add contact info Publications: for this service. This can be a URI to the publication and/or a DOI. None Login to add publication info Citations: None Login to add a citation