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. 2007 Dec 5;2007(1):14741. doi: 10.1155/2007/14741

Identifying Statistical Dependence in Genomic Sequences via Mutual Information Estimates

Hasan Metin Aktulga 1,✉, Ioannis Kontoyiannis 2, L Alex Lyznik 3, Lukasz Szpankowski 4, Ananth Y Grama 1, Wojciech Szpankowski 1
PMCID: PMC3171327  PMID: 18301721

Abstract

Questions of understanding and quantifying the representation and amount of information in organisms have become a central part of biological research, as they potentially hold the key to fundamental advances. In this paper, we demonstrate the use of information-theoretic tools for the task of identifying segments of biomolecules (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, they are used for the identification of correlations between different parts of the maize zmSRp32 gene. There, we find significant dependencies between the Inline graphic untranslated region in zmSRp32 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 the FBI's combined DNA index system (CODIS), we demonstrate that our approach is particularly well suited for the problem of discovering short tandem repeats—an application of importance in genetic profiling.

[1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22]

Contributor Information

Hasan Metin Aktulga, Email: haktulga@cs.purdue.edu.

Ioannis Kontoyiannis, Email: yiannis@aueb.gr.

L Alex Lyznik, Email: alex.lyznik@pioneer.com.

Lukasz Szpankowski, Email: lszpanko@bioinf.ucsd.edu.

Ananth Y Grama, Email: ayg@cs.purdue.edu.

Wojciech Szpankowski, Email: spa@cs.purdue.edu.

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