MiniMiner      
Binary files Source code Manual
 
 


Phylogenetic motifs (PMs) predict protein functional site predictions from sequence alignments. Their predictive power has been demonstrated in many investigations, especially as applied to ligand-binding and active site regions.
The software miniMINER is a streamlined and self-contained tool for PM identification.
Download the complete package
 
  Files to download
You can access the redistributable file list in sourceforge file list or use the following direct links: The latest versions of source files are available via sourceforge subversion and can be browsed in its repository browser.
 
  A common miniMINER example
The most common use of miniMINER is to calculate phylogenetic similarity scores (PSZ) that quantify phylogenetic similarity; more negative scores indicate greater similarity. miniMINER outputs a PSZ score for each window of an input alignment using the following syntax:

java -jar miniminer-1.2.0.jar -m [options] inputfile

The options are described fully within the user’s manual. Note that webMINER, which includes several data visualization options, can be accessed at: http://coit-apple01.uncc.edu/MINER.
 
  References
  • La D, Sutch B, Livesay DR (2005). Predicting protein functional sites with phylogenetic motifs. Proteins, 58:309-320.
  • Roshan U, Livesay DR, La D (2005). Improved phylogenetic motif identification using parsimony. Fifth IEEE Symposium on Bioinformatics and Bioengineering, BIBE05:19-26.
  • La D, Livesay DR (2005). Accurate functional site prediction using an automated algorithm suitable for heterogeneous datasets. BMC Bioinformatics, 6:116.
  • La D, Livesay DR (2005). MINER: software for phylogenetic motif identification. Nucleic Acids Research, 33:W267-W270.
  • KC DB, Livesay DR (2008). Improving position specific predictions of protein functional sites using phylogenetic motifs. Bioinformatics, 24:2308-2316.
  • KC DB, Livesay DR. Topology improves phylogenetic motif functional site predictions. IEEE/ACM Transactions on Computational Biology and Bioinformatics, In press.
 
  Last updated: 3/9/210