SPAR is designed for prediction and analysis of self-interaction prediction. If you want to use it in your local computer, the guide for installation is as follows:
1). Get the current tarball of the latest HMMER3 release from the HMMER site.
2). Uncompress the tarball
shell% tar -zxvf hmmer-3.1b1.tar.gz
3). Adding HMMER3 binaries to your path
bash% export PATH=/path/to/install/hmmer3/binaries:$PATHDownload Pfam data files
1). You need to download the following files from the Pfam FTP site:
2). You need to generate binary files for Pfam-A.hmm by running the following commands:
shell% hmmpress Pfam-A.hmmInstall Python dependencies
The spar.py depends on several packages that don't come as part of a standard Python distribution, notably Numpy, Scipy, Biopython and Scikit-learn. Everything that you need can be installed via "pip" tool:
shell% pip install numpy
shell% pip install scipy
shell% pip install biopython
shell% pip install scikit-learnUnpack the script
shell% tar zxvf spar.tar.gz
shell% cd sparInterpretation of Result
1. "+" means the site in the domain-domain interaction (DDI) in the specified PDB code. In addition, The uppercase in the consensus sequence (#HMM) indicates that this site is more conserved than others. These sites was regarded as critical resides for the protein self-interaction.
2. The DDI information was referred to the iPfam, if you want get the whole self-interacting domain, click here to download the original materials.
3. If you want to get more detail about the DDI information, please click here to visit the 3did database.