Statistical dependence in biological sequences

We demonstrate the use of information-theoretic tools for the task of identifying segments of hiomolecules (DNA or RNA) that are statistically correlated. We develop a precise and reliable methodology, based on the notion of mutual information, for finding and extracting statistical as well as structural dependencies. A simple threshold function is defined, and its use in quantifying the level of significance of dependencies between biological segments is explored. These tools are used in two specific applications. First, for the identification of correlations between different parts of the maize zmSRp32 gene. There, we find significant dependencies between the 5' untranslated region and its alternatively spliced exons. This observation may indicate the presence of as-yet unknown alternative splicing mechanisms or structural scaffolds. Second, using data from CODIS, we demonstrate that our approach is well suited for the problem of discovering short tandem repeals (STRs). ©2007 IEEE