mkdom2 is the program we use routinely to build each new release of ProDom.The algorithm is described elsewhere (Gouzy et al., 1999), but let’s briefly say that it 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. For building ProDom, we run this program on the UniProt (swissprot/trembl) Knowledge Database, but it can be run on any set of protein sequences (as long as you have a fasta file).
- a file containing the sequences to analyse in fasta format
- parameters. default will be -j 10 -e 0.01 -h 0.01. If you are happy with that, please don’t write anything into that filed, just let it empty. 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 XS
- the project file used to launch xdom faster.We have a perl script available here to run this webservice from your computer. Please install SOAP Lite before .
To download xdom go to : http://prodom.prabi.fr/prodom/current/html/download.phpTo run mkdom2 directly on your computer, we suggest you download the mkdom2 program and use the onlinehelp instead of using this webservice. This webservice is created to use within workflows.