On DNA Codes

On DNA Codes We develop and study the concept of similarity functions for q-ary sequences. For the case q = 4, these functions can be used for a mathematical model of the DNA duplex energy [1,2], which has a number of applications in molecular biology. Based on these similarity functions, we define a concept of DNA codes [1]. We give brief proofs for some of our unpublished results [3] connected with the well-known deletion similarity function [4–6]. This function is the length of the longest common subsequence; it is used in the theory of codes that correct insertions and deletions [5]. Principal results of the present paper concern another function, called the similarity of blocks. The difference between this function and the deletion similarity is that the common subsequences under consideration should satisfy an additional biologically motivated [2] block condition, so that not all common subsequences are admissible. We prove some lower bounds on the size of an optimal DNA code for the block similarity function. We also consider a construction of close-to-optimal DNA codes which are subcodes of the parity-check one-error-detecting code in the Hamming metric [7]. http://www.deepdyve.com/assets/images/DeepDyve-Logo-lg.png Problems of Information Transmission Springer Journals

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Publisher
Springer Journals
Copyright
Copyright © 2005 by MAIK "Nauka/Interperiodica"
Subject
Engineering; Communications Engineering, Networks; Electrical Engineering; Information Storage and Retrieval; Systems Theory, Control
ISSN
0032-9460
eISSN
1608-3253
D.O.I.
10.1007/s11122-006-0004-3
Publisher site
See Article on Publisher Site

Abstract

We develop and study the concept of similarity functions for q-ary sequences. For the case q = 4, these functions can be used for a mathematical model of the DNA duplex energy [1,2], which has a number of applications in molecular biology. Based on these similarity functions, we define a concept of DNA codes [1]. We give brief proofs for some of our unpublished results [3] connected with the well-known deletion similarity function [4–6]. This function is the length of the longest common subsequence; it is used in the theory of codes that correct insertions and deletions [5]. Principal results of the present paper concern another function, called the similarity of blocks. The difference between this function and the deletion similarity is that the common subsequences under consideration should satisfy an additional biologically motivated [2] block condition, so that not all common subsequences are admissible. We prove some lower bounds on the size of an optimal DNA code for the block similarity function. We also consider a construction of close-to-optimal DNA codes which are subcodes of the parity-check one-error-detecting code in the Hamming metric [7].

Journal

Problems of Information TransmissionSpringer Journals

Published: Jan 23, 2006

References

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