Study of DNA binding sites using the Rényi parametric entropy measure

Shannonʹs definition of uncertainty or surprisal has been applied extensively to measure the information content of aligned DNA sequences and characterizing DNA binding sites. In contrast to Shannonʹs uncertainty, this study investigates the applicability and suitability of a parametric uncertainty measure due to Rényi. It is observed that this measure also provides results in agreement with Shannonʹs measure, pointing to its utility in analysing DNA binding site region. For facilitating the comparison between these uncertainty measures, a dimensionless quantity called “redundancy” has been employed. It is found that Rényiʹs measure at low parameter values possess a better delineating feature of binding sites (of binding regions) than Shannonʹs measure. The critical value of the parameter is chosen with an outlier criterion.