In this paper, we address two ways of difference expansion based reversible DNA watermarking using noncoding DNA sequence. Unlike image data, the reversible DNA watermarking should consider the string structure of a DNA sequence, the organism functionality, the perfect recovery, and the high embedding capacity. We convert the string sequence of four characters in noncoding region to the decimal...

The LpS1 alpha and beta genes of Lytechinus pictus are activated at the late cleavage stage of embryogenesis, with LpS1 mRNAs accumulating only in lineages contributing to aboral ectoderm. We had shown previously that 762 bp of 5' flanking DNA from the LpS1 beta gene was sufficient for proper temporal and aboral ectoderm specific expression. In the present study, we identified a strong positive...

Transversal vibrations of an axially moving string under boundary damping are investigated. Mathematically, it represents a homogenous linear partial differential equation subject to nonhomogeneous boundary conditions. The string is moving with a relatively (low) constant speed, which is considered to be positive.  The string is kept fixed at the first end, while the other end is tied with the ...

In this paper we present external memory algorithms for some string problems. External memory algorithms have been developed in many research areas, as the speed gap between fast internal memory and slow external memory continues to grow. The goal of external memory algorithms is to minimize the number of input/output operations between internal memory and external memory. These years the sizes...

We study algorithms for solving a problem of constructing text (a long string) from dictionary sequence small strings). The has an application in bioinformatics and connection with the assembly method reconstructing DNA fragments. Our is construction string t length n using strings $$s^1,\dots , s^m$$ possible overlapping. Firstly, we provide classical (randomized) algorithm running time $$O\le...

In this work we study string kernel methods for sequence analysis and focus on the problem of species-level identification based on short DNA fragments known as barcodes. We introduce efficient sorting-based algorithms for exact string k-mer kernels and then describe a divide-and-conquer technique for kernels with mismatches. Our algorithm for the mismatch kernel matrix computation improves cur...

In DNA related research, due to various environment conditions, mutations occur very often, where a mutation is defined as a heritable change in the DNA sequence. Therefore, approximate string matching is applied to answer those queries which find mutations. The problem of approximate string matching is that given a user specified parameter, k, we want to find where the substrings, which could ...

In this paper, we discuss an efficient and effective index mechanism to support the matching of massive pattern strings in against a very long target string. It is very important to the next generation sequencing in the biological research. The main idea behind it is to construct an automaton over all the pattern strings, and search the automaton against a BWT-array L created for a target strin...

An interactive tool to visualize the K-string composition of long DNA sequences including bacterial complete genomes is described. It is especially useful for exploring short palindromic structures in the sequences. The SeeDNA program runs on Red Hat Linux with GTK+ support. It displays two-dimensional (2D) or one-dimensional (1D) histograms of the K-string distribution of a given sequence and/...