Alignment of protein domains with MDAT: Any suggestions?

Question

[cavelandiah]

Hi guys, I was wondering to know if some of you have used MDAT program (http://www.bornberglab.org/pages/mdat), this is an aligner for protein domains. But it seems to be a little bit old and there are no good descriptions of the way to use it. The --help flag gave me:

[faf43525@52563es1 MDAT]$ /usr/local/bin/mdat --help
MDA v1.0  Copyright (C) 2013,2014  Carsten Kemena
This program comes with ABSOLUTELY NO WARRANTY;

Allowed options are displayed below.:

General options:
 -h [ --help ]                  Produces this help message
 -s [ --sequence ] arg          Sequence file
 -d [ --domain_f ] arg          Domain file
 -o [ --msa_out ] arg           File to write the MSA to.
 -a [ --mda_out ] arg           File to write the MDA to.
 -f [ --format ] arg (=fasta)   Output format for the MSA
 -t [ --threads ] arg (=1)      Number of threads to use

Some ideas to use it? do not know what is i.e Domain file. Because the flag --domain_f is mandatory. Thanks a lot.

[GenoMax]

Take a look at the README.md file included in the distribution. It says this:

Certain data is need by MDAT. For it to be found automatically you need to copy the content of the folder data into a (hidden) folder in your home named ".mdat". Alternatively you can give the domain math probably matrix manually using the '--dmpm_f' option.

Even though there is a doc folder in the distro it seems to mainly contain information about software and not how to use it.