Data used

• Phylogenetic profiles for 2,465 genes of the yeast Saccharomyces cerevisiae BLASTed against 24 genomes. The values in this file represent "-log(E-value)". In the paper, each bit of the phylogenetic profile was set to 0 if this number is negative (E-value > 1), 1 otherwise.
• Functional categories(HTML or Texte) downloaded from the Munich Information Center for Protein Sequence Comprehensive Yeast Genome Database (CYGD)

Software

The SVM and kernel computations are based on the software SVM Light v.3.50 by Thorsten Joachims. We added the following files:

• kernel.c
• compute_gram.c

and modified the file:

• kernel.h
• Makefile

After compiling SVM Light with the modified files, you should be able to use it with the option "-t 4" (user defined kernel, see the SVM Light documentation).

Warning: the kernel in kernel.c contains the definition of the Bayesian tree model for the particular example studied in this paper. If you want to use it for an other data set, don't forget to modify this file accordingly (or to rewrite it in a cleaner way...).

Useful PERL script

• prep.pl: prepares positive and negative example files for SVMLight from the phylogenetic profile file (with -log(E-value)) and a MIPS category text file
• randsplit.pl: randomly splits a file into two files (line by line)
• test.pl: performs the experiment described in the reference paper, which consists in comparing the performance of a SVM with a linear kernel and with the tree kernel on the prediction of the MIPS categories

Results

• The directory here contains the ROC curves for each MIPS class.
• The file roc50 contains the roc50 index for all MIPS classes, sorted by decreasing performance for the linear SVM.