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Evaluation of genetic test redundancy using a high-frequency component of the l-gram graph

Evaluation of genetic test redundancy using a high-frequency component of the l-gram graph

Biofizika 44(4): 639-648

Various approaches to the estimation of DNA redundancy are compared: the Shannon entropy, the Lempel-Ziv complexity, and a new method, the computation of the low-frequency component of the l-gram graph. Although these methods are based on different ideas, they satisfy some reasonable requirements. The ability of these methods to find various kinds of repeats in genetic texts is compared. The resolution of the new method for calculation of DNA redundancy is discussed on the example of well-known repeats in the Epstein-Barr virus genome. The intrinsic discrepancy of high-frequency profile and Shannon redundancy profile were observed in some functionally significant regions of sequences being investigated.

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Accession: 046010055

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PMID: 10544814

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