A mutual information kernel for sequences

We propose a new kernel for strings which borrows ideas and techniques from information theory and data compression. This kernel can be used in combination with any kernel method, in particular support vector machines for protein classification. By incorporating prior assumptions on the properties of the alphabet and using a Bayesian averaging framework, we compute the value of this kernel in linear time and space, benefiting from previous achievements proposed in the field of universal coding. Encouraging classification results are reported on a standard protein homology detection experiment.