Recognition sites for type II restriction and modification enzymes in genomes of 
several bacteria are recognized as semi-palindromic motifs and are avoided at a 
significant degree. The key idea of contrast word analysis with respect to RMS 
recognition sites, is that under-represented words are likely to be selected 
against. Starting from over- or underrepresented words corresponding to RMS 
recognition sites in specific clades, the specificity of unknown R-M systems can 
be highlighted. Among the known restriction enzymes, that are described in the 
REBASE database of restriction and modification systems, many of their 
recognition sites are still uncharacterized. Eventually, this motivates studies 
aimed at assessing horizontal transferring events of RMS in micro-organisms 
through the analysis of word usage biases in well-determined genomic regions. A 
probabilistic model is built on a first-order Markovian chain. Statistics on the 
k-neighborhood of a word is carried out to assess the biological significance of 
a genomic motif. Efficient word counting procedures have been implemented and 
statistics are used for the assessment of the significance of individual words 
in large sequences. On the basis of the set of most avoided words, and in 
accordance to the IUPAC coding standards, suggestions are made regarding 
potential recognition sequences. In certain cases, a comparison of avoided 
palindromic words in taxonomically related bacteria shows a pattern of 
relatedness of their R-M systems. For strengthening this analysis, the primary 
protein structure of all type II R-M systems known in REBASE have been blasted 
against the nr-GENBANK database. The combination of these analyses has revealed 
some interesting examples of possible horizontal transfer events of R-M systems.