Reverse-complement similarity codes

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], © Springer-Verlag Berlin Heidelberg 2006 sequences, subsequences, similarity, DNA sequences, codes, code distance, rate of codes, insertion-deletion codes.