Analysis of DNA-Dimer Frequency in Retroviral Genomes with a Fuzzy Itemsets Pattern Induction Strategy

Since DNA dimer analysis has demonstrated to provide a very conserved pattern that has been suggested as a genome signature, we apply a strategy based on fuzzy sets theory and frequent itemsets pattern induction, for searching hidden structural relations in the DNA-dimer frequency patterns of a collection of Retrovirus genomes. We found an interesting differentiation between subsets of retroviruses, as well as some unexpected similarities in the context of the DNA-dimer frequency patterns. We believe that identifying basic genomic patterns and connecting this information with other sources of information can give us new and important knowledge about how these patterns are related with the viral structure and its dynamics. The computational methodology presented in this paper has demonstrated to be a robust tool for the study and the analysis of genomic sequences.