It is shown that metric representation of DNA sequences is one-to-one. By using the metric representation method, suppression of nucleotide strings in the DNA sequences is determined. For a DNA sequence, an optimal string length to display genomic signature in chaos game representation is obtained by eliminating effects of the finite sequence. The optimal string length is further shown as a sel...

We introduce and investigate an operation with strings suggested by DNA processing (by means of exonucleases): the operation of cutting strings of equal length from the beginning and the end of a string. A related operation is that of cutting a square of a string from the preex of a string. The closure properties of families in the Chomsky hierarchy are investigated (and, with one exception, fo...

Searching for DNA or amino acid sequences similar to a given pattern string is very important in molecular biology. In fact, a lot of programs and algorithms have been developed. Most of them are based on alignment of strings or approximate string matching. However, they do not seem to be adequate in some cases. For example, the DNA pattern TATA (known as TATA box) is a common promoter that oft...

A suffix tree (also called suffix trie, PAT tree or, position tree) is a powerful data structure that presents the suffixes of a given string in a way that allows a fast implementation of important string operations. The idea behind suffix trees is to assign to each symbol of a string an index corresponding to its position in the string. The first symbol in the string will have the index 1, the...

In this research, dynamic analysis of the rotational slender axially moving string is investigated. String assumed as Euler Bernoulli beam. The axial motion of the string, gyroscopic force and mass eccentricity were considered in the study. Equations of motion are derived using Hamilton’s principle, resulting in two partial differential equations for the transverse motions. The equations are ch...

The problem of approximate string searching comprises two classes of problems: string searching with k mismatches and string searching with k differences. In this paper we present a short survey and experimental results for well known sequential approximate string searching algorithms. We consider algorithms based on different approaches including dynamic programming, deterministic finite autom...

S-box is one of the most significant structures used to construct encryption that strong and resistant attacks in algorithms. The new 4D-hyper chaotic system deoxyribonucleic acid (DNA) computing are this paper provide a dynamic generating approach. 4D generated numbers processed generate hexadecimal number will encode using DNA coding method addition, subtraction, exclusive-or operations produ...

In this paper we study a generalization of the classical notions of bordered and unbordered words, motivated by DNA computing. DNA strands can be viewed as finite strings over the alphabet {A, G, C, T}, and are used in DNA computing to encode information. Due to the fact that A is Watson-Crick complementary to T and G to C, DNA single strands that are Watson-Crick complementary can bind to each...

Studying patterns in DNA sequences has been for years the subject of many research papers in bioinformatics. This paper evaluates two algorithms used for DNA comparison. Those are: Longest Common Substring and Subsequence (LCS, LCSS). Evaluation is performed based on the different code implementations for those two algorithms. Accuracy and performance are the two major criteria that are used fo...