1. DownloadYou can download a tar file here. After downloading, the file needs to be decompressed:
> tar -xvzf MotifHound_130801.tar.gz
> cd MotifHound/
2. Third party librariesIn order to work with S. cerevisiae and H. sapiens datasets, we also provide precomputed data on disorder, Pfam domains, evolution and function descriptions. These data are not required to run MotifHound but they are recommended to use it with its full potential. These data can be downloaded here and copied in the "data" directory of MotifHound.
Importantly, MotifHound uses the following programs/libraries that need to be installed:
- "Judy arrays" is a C library that can be either installed with the following command on Ubuntu systems:
> sudo apt-get install libjudydebian1
alternatively, the source of this library can be downloaded here.
- blast is required if masking of homologous regions is desired. It can be installed with the following command on Ubuntu systems:
> sudo apt-get install Blast2
alternatively, please refer to the NCBI blast pages for other installation instructions.
- Some Perl modules are also necessary, for this we recommend to use the following commands:
> sudo apt-get install perl cpanminus
> sudo cpanm Tk Tk::TableMatrix File::Basename File::Copy List::MoreUtils Cwd Getopt::Long FindBin Benchmark
3. Running the programFollowing these installs, you can then run MotifHound with the following command (and may configure the options as you want):
> perl ./Scripts/MotifHound.pl --Setfile ./Data/Seq/Set/YEAST_Set_TEST.faa --Proteome ./Data/Seq/Proteome/YEAST_Proteome_TEST.fasta --Size 3 10 --Scan --WD ./Results --H --Blastfile ./Data/Blast/Blast_YEAST_Proteome.blast --D --Disofile ./Data/Disorder/YEAST_Proteome_DISORDER.dat --Pfam_annot ./Data/Domains/YEAST_Proteome_Pfam_Domains.txt --Gene_annot ./Data/Genes/YEAST.data --HTML
To display the help :
> perl ./Scripts/MotifHound.pl --help