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Pairwise sequence alignment is a central problem in bioinformatics, which forms the basis of various other applications. Two related sequences are expected to have a high alignment score, but relatedness is usually judged by statistical significance rather than by alignment score. Recently, it was shown that pairwise statistical significance gives promising results as an alternative to database statistical...
Nucleosome, a nucleoprotein structure formed by coiling 147bp of DNA around an octamer of histone proteins, is the fundamental repeating unit of eukaryotic chromatin. By regulating the access of biological machineries to underlying \textit{cis}-regulatory elements, its mobility has been implicated in many important cellular processes. Although it has been known that various factors, such as DNA sequences,...
DNA sequences are often found to be composed of locally homogeneous segments that are functionally important. Most sequence comparison methods do not consider such a compositional property. We introduce a new method that takes this issue into consideration. With our method, the information of a DNA sequence is first transformed into a multi-order transition matrix (MTM); the resulting matrices are...
This paper firstly gives a brief overview of information embedding in deoxyribonucleic acid (DNA) sequences and its applications. DNA data embedding can be considered as a particular case of communications with or without side information, depending on the use of coding or noncoding DNA sequences, respectively. Although several DNA data embedding methods have been proposed over the last decade, it...
Recent development of molecular biological tools has created several research fields such as systems biology, omics studies, and molecular diagnostics. Among them, molecular diagnostics is a new area of clinical diagnosis, and it includes all tests and methods to identify a disease or the predisposition for a disease analyzing DNA, RNA or proteins of an organism. After completion of the human genome...
Biological processes in organisms are driven by the genetic code represented by sequences of DNA. Every cell of a multi-cellular organism contains the full genome; however the gene activations differ based on a variety of factors at varying parts of the organism. The genetic code can be seen as an omni-functional code that is primarily function-agnostic, but triggers its relevant and required genes...
We applied mode-decomposition and matched-filtering, both signal processing techniques used to increase the signal-to-noise ratio (SNR), to array CGH data of human meningioma DNA, in order to extract genomic regions of copy-number changes potentially associated with tumor progression. DNA segments from different chromosomes were decomposed into a small number of dominant components (modes), and low-amplitude...
Isochore is one of the most striking features of the DNA sequences of warm-blooded animals. Isochores affect both coding and non-coding sequences and reflect a fundamental level of genome organization. In this paper, a new method (GCDT) is introduced to display the isochore structures. This method not only can illustrate the isochore structures very well, but also can provide a more detailed description...
It has very important significance to research non- coding region and its function. The Z curve is a very usefui method for visuaiizing and anaiyzing DNA sequences. It is a three-dimensionai space curve constituting the unique representation of a given DNA sequence in the sense that each can be uniquely reconstructed from the other. Based on the Z curve, a new non-coding RNA-flnding method for some...
Microarray is widely used for the cancer research and identifies different expressions for specific genes. We present a computational method for constructing cancer and normal gene regulatory networks from micorarray data based on transcription factor analysis and independency test. The web service technology is used to wrap the bioinformatics toolkits of methods and databases to automatically extract...
In eukaryotic cells, genomic DNAs wrap around beadlike molecules, called nucleosomes, so as to pack more compactly in the nucleus of the cell. The nucleosome is made up of four pairs of histone proteins (H2A, H2B, H3, and H4) who share a very similar structural motif. The positioning of nucleosomes as well as the modifications of various sites of histone proteins (such as acetylation) plays important...
Processing of DNA sequences using traditional digital signal processing methods requires their conversion from a character string into numerical sequences as a first step. Many representations introduced previously assign values to indicate the four DNA nucleotides A, C, G, and T that impose mathematical structures not present in the actual DNA sequence. In this paper, almost all existing methods...
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