Efficient reconstruction of sequences from their subsequences or supersequences
Journal of Combinatorial Theory Series A
A weighted insertion-deletion stacked pair thermodynamic metric for DNA codes
DNA'04 Proceedings of the 10th international conference on DNA computing
IEEE Transactions on Information Theory
Successful preparation and analysis of a 5-site 2-variable DNA library
Natural Computing: an international journal
DNA codes for additive stem similarity
Problems of Information Transmission
DNA codes based on stem similarities between DNA sequences
DNA13'07 Proceedings of the 13th international conference on DNA computing
On volumes of spheres for the stem distance
Problems of Information Transmission
On enumeration of q-ary sequences with a fixed number of occurrences of the subblock 00
Problems of Information Transmission
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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 We give brief proofs for some of our unpublished results [3] connected with the well-known deletion similarity function [4---6].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].