This paper presents a detail description of a new DNA-based cryptographic key generation algorithm that can be used to generate strong cryptographic key(s) for symmetric ciphering applications. The algorithm uses an initial private/secret key as an input to the Key-Based Random Permutation (KBRP) algorithm to generate a permutation of size n, which is half of the size of the required cryptograp...

There are plenty specific types of data which are needed to compress for easy storage and to reduce overall retrieval times. Moreover, compressed sequence can be used to understand similarities between biological sequences. DNA data compression challenge has become a major task for many researchers for the last few years as a result of exponential increase of produced sequences in gene database...

For aligning DNA sequences that differ only by sequencing errors, or by equivalent errors from other sources, a greedy algorithm can be much faster than traditional dynamic programming approaches and yet produce an alignment that is guaranteed to be theoretically optimal. We introduce a new greedy alignment algorithm with particularly good performance and show that it computes the same alignmen...

Since the advent of rapid DNA sequencing methods in 1976, scientists have had the problem of inferring DNA sequences from sequenced fragments. Shotgun sequencing is a well-established biological and computational method used in practice. Many conventional algorithms for shotgun sequencing are based on the notion of pairwise fragment overlap. While shotgun sequencing infers a DNA sequence given ...

Biological pairwise sequence alignment can be used as a method for arranging two biological characters to identify regions of similarity. This operation has elicited considerable interest due its significant influence on various critical aspects life (e.g., identifying mutations in coronaviruses). Sequence over large databases cannot yield results within reasonable time, power, and cost. heuris...

The importance of DNA sequence design for reliable DNA computing is well recognized. In this paper, we describe a DNA sequence optimization system NACST/Seq that is based on a multiobjective genetic algorithm. It uses the concept of Pareto optimization to reflect many realistic characteristics of DNA sequences in real bio-chemical experiments flexibly. This feature allows to recommend multiple ...

Data compression is concerned with how information is organized in data. The size and importance of these databases will be bigger and bigger in the future; therefore this information must be stored or communicated efficiently though there are many text compression algorithms, they are not well suited for the characteristics of DNA sequences. There are algorithms for DNA compression which takes...

In this paper, we propose an efficient hierarchical DNA sequence search method to improve the search speed while the accuracy is being kept constant. For a given query DNA sequence, firstly, a fast local search method using histogram features is used as a filtering mechanism before scanning the sequences in the database. An overlapping processing is newly added to improve the robustness of the ...