PRABI – Rhone-Alpes Bioinformatics Center


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

Base URL:

WSDL Location: last cached WSDL file)

Documentation URL(s): ProDom team (about 1 year ago)

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.



    • 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.



  • 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


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