Reverse–complement similarity codes

Authors:
A. D'yachkov;D. Torney;P. Vilenkin;S. White
Affiliations:
-;-;-;-
Venue:
General Theory of Information Transfer and Combinatorics
Year:
2006

Citing 3
Cited 0

Mathematical Methods for DNA Sequences

Mathematical Methods for DNA Sequences
A weighted insertion-deletion stacked pair thermodynamic metric for DNA codes

DNA'04 Proceedings of the 10th international conference on DNA computing
On similarity codes

IEEE Transactions on Information Theory

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Abstract

In this paper, we discuss a general notion of similarity function between two sequences which is based on their common subsequences. This notion arises in some applications of molecular biology [14]. We introduce the concept of similarity codes and study the logarithmic asymptotics for the size of optimal codes. Our mathematical results announced in [13] correspond to the longest common subsequence (LCS) similarity function [2] which leads to a special subclass of these codes called reverse-complement (RC) similarity codes. RC codes for additive similarity functions have been studied in previous papers [9,10,11,12].