Study of DNA binding sites using the Rényi parametric entropy measure.
Shannon's 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 Shannon's 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 Shannon's 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 Rényi's measure at low parameter values possess a better delineating feature of binding sites (of binding regions) than Shannon's measure. The critical value of the parameter is chosen with an outlier criterion.
Krishnamachari
A
A
Bioinformatics Centre, Jawaharlal Nehru University, New Delhi 110 067, India.
moy Mandal
Vijnan
V
Karmeshu
D000818:Animals; D001665:Binding Sites; D004247:DNA / Q000378:metabolism*; D019277:Entropy; D007257:Information Theory; D008954:Models, Biological
D004247:DNA