scholarly journals The self-similarity properties and multifractal analysis of DNA sequences

2019 ◽  
Vol 4 (1) ◽  
pp. 267-278 ◽  
Author(s):  
G. Durán-Meza ◽  
J. López-García ◽  
J.L. del Río-Correa
Keyword(s):  
Hausdorff Dimension ◽  
Dna Sequence ◽  
Dna Sequences ◽  
Multifractal Analysis ◽  
Deoxyribonucleic Acid ◽  
Point Of View ◽  
The Self ◽  
Hölder Exponent ◽  
Self Similarity ◽  
Multifractal Decomposition

AbstractIn this work is presented a pedagogical point of view of multifractal analysis deoxyribonucleic acid (DNA) sequences is presented. The DNA sequences are formed by 4 nucleotides (adenine, cytosine, guanine, and tymine). Following Jeffrey’s paper we associated a simple contractive function to each nucleotide, and constructed the Hutchinson’s operator W, which was used to build covers of different sizes of the unitary square Q, thus Wk(Q) is a cover of Q, conformed by 4k squares Qk of size 2−k, as each Qk corresponds to a unique subsequence of nucleotides with length k : b1b2...bk. Besides, it is obtained the optimal cover Ck to the fractal F generated for each DNA sequence was obtained. We made a multifractal decomposition of Ck in terms of the sets Jα conformed by the Qk’s with the same value of the Holder exponent α, and determined f (α), the Hausdorff dimension of Jα, using the curdling theorem.

Scaled Fuzzy Graph for Cluster Analysis in DNA Sequence of Olfactory Receptors

2013 ◽  
Vol 8 (1) ◽  
pp. 57-70
Author(s):  
Satya Ranjan Dash ◽  
Satchidananda Dehuri ◽  
Uma Kant Sahoo
Keyword(s):  
Cluster Analysis ◽  
Dna Sequence ◽  
Simulation Study ◽  
Dna Sequences ◽  
Clustering Algorithm ◽  
Deoxyribonucleic Acid ◽  
Graph Model ◽  
Olfactory Receptors ◽  
Fuzzy Graph ◽  
Before And After

Olfactory receptors (ORs) are responsible for recognition of odor molecules. The deoxyribonucleic acid (DNA) sequences of these receptors are severely affected by local mutations. Therefore, to study the changes among affected and non-affected ORs, the authors attempted to use unsupervised learning (clustering) algorithm. In this paper, they have used a scaled fuzzy graph model for clustering to study the changes before and after the local mutation on DNA sequences of ORs. Their simulation study at the fractional dimensional level confirms its accuracy.

scholarly journals Evolution of the Periodicity and the Self-Similarity in DNA Sequence: A Fourier Transform Analysis.

2001 ◽  
Vol 51 (2) ◽  
pp. 159-168 ◽  
Author(s):  
Naoki Nagai ◽  
Kazuo Kuwata ◽  
Tomoya Hayashi ◽  
Hiromi Kuwata ◽  
Seiichi Era
Keyword(s):  
Fourier Transform ◽  
Dna Sequence ◽  
The Self ◽  
Self Similarity

scholarly journals Deoxyribonucleic acid methylation and chromatin organization in Tetrahymena thermophila.

1981 ◽  
Vol 1 (7) ◽  
pp. 600-608 ◽  
Author(s):  
K Pratt ◽  
S Hattman
Keyword(s):  
Dna Replication ◽  
Dna Sequence ◽  
Dna Sequences ◽  
Cytosine Methylation ◽  
Deoxyribonucleic Acid ◽  
Tetrahymena Thermophila ◽  
Staphylococcal Nuclease ◽  
Chromatin Organization ◽  
Deoxyribonuclease I ◽  
Cell Biol

Deoxyribonucleic acid (DNA) of the transcriptionally active macronucleus of Tetrahymena thermophila is methylated at the N6 position of adenine to produce methyladenine (MeAde); approximately 1 in every 125 adenine residues (0.8 mol%) is methylated. Transcriptionally inert micronuclear DNA is not methylated (< or = 0.01 mol% MeAde; M. A. Gorovsky, S. Hattman, and G. L. Pleger, J. Cell Biol. 56:697-701, 1973). There is no detectable cytosine methylation in macronuclei in Tetrahymena DNA (< or = 0.01 mol% 5-methylcytosine). MeAde-containing DNA sequences in macronuclei are preferentially digested by both staphylococcal nuclease and pancreatic deoxyribonuclease I. In contrast, there is no preferential release of MeAde during digestion of purified DNA. These results indicate that MeAde residues are predominantly located in "linker DNA" and perhaps have a function in transcription. Pulse-chase studies showed that labeled MeAde remains preferentially in linker DNA during subsequent rounds of DNA replication; i.e., there is little, if any, movement of nucleosomes during chromatin replication. This implies that nucleosomes may be phased with respect to DNA sequence.

scholarly journals A Color-Image Encryption Scheme Using a 2D Chaotic System and DNA Coding

2019 ◽  
Vol 2019 ◽  
pp. 1-13
Author(s):  
Haidar Raad Shakir
Keyword(s):  
Dna Sequence ◽  
Dna Sequences ◽  
Deoxyribonucleic Acid ◽  
Color Image ◽  
Color Image Encryption ◽  
Chaotic Sequences ◽  
Xor Operation ◽  
Password Protection ◽  
Differential Attacks ◽  
Exclusive Or

This paper proposes a method of encrypting images with password protection for secure sharing based on deoxyribonucleic acid (DNA) sequence operations and the tangent-delay ellipse reflecting the cavity-map system (TD-ERCS). The initial values of the TD-ERCS system are generated from a user’s password, and the TD-ERCS system is used to scramble the pixel locations of the R, G, and B matrices of the original image. Next, three DNA-sequence matrices are generated by encoding the permuted color image such that it can be transformed into three matrices. Then, the TD-ERCS system is employed to generate three chaotic sequences before encoding the DNA into the three matrices. Thereafter, a DNA exclusive OR (XOR) operation is executed between the DNA sequences of the permuted image and the DNA sequences generated by the TD-ERCS system to produce three encrypted scrambled matrices. Finally, the matrices of the DNA sequences are decoded, and the R, G, and B channels are recombined to form an encrypted color image. The results of simulation and security tests reveal that the proposed algorithm offers robust encryption and demonstrates the ability to resist exhaustive, statistical, and differential attacks.

scholarly journals On Khintchine exponents and Lyapunov exponents of continued fractions

2009 ◽  
Vol 29 (1) ◽  
pp. 73-109 ◽  
Author(s):  
AI-HUA FAN ◽  
LING-MIN LIAO ◽  
BAO-WEI WANG ◽  
JUN WU
Keyword(s):  
Hausdorff Dimension ◽  
Lyapunov Exponents ◽  
Continued Fractions ◽  
Multifractal Analysis ◽  
Continued Fraction ◽  
Constant Function ◽  
Point Of View ◽  
Lyapunov Spectrum ◽  
Continued Fraction Expansion

AbstractAssume that x∈[0,1) admits its continued fraction expansion x=[a1(x),a2(x),…]. The Khintchine exponent γ(x) of x is defined by $\gamma (x):=\lim _{n\to \infty }({1}/{n}) \sum _{j=1}^n \log a_j(x)$ when the limit exists. The Khintchine spectrum dim Eξ is studied in detail, where Eξ:={x∈[0,1):γ(x)=ξ}(ξ≥0) and dim denotes the Hausdorff dimension. In particular, we prove the remarkable fact that the Khintchine spectrum dim Eξ, as a function of $\xi \in [0, +\infty )$, is neither concave nor convex. This is a new phenomenon from the usual point of view of multifractal analysis. Fast Khintchine exponents defined by $\gamma ^{\varphi }(x):=\lim _{n\to \infty }({1}/({\varphi (n)}))\sum _{j=1}^n \log a_j(x)$ are also studied, where φ(n) tends to infinity faster than n does. Under some regular conditions on φ, it is proved that the fast Khintchine spectrum dim ({x∈[0,1]:γφ(x)=ξ}) is a constant function. Our method also works for other spectra such as the Lyapunov spectrum and the fast Lyapunov spectrum.

FPGA Based Data Hiding Methods using DNA Cryptography Techniques

2016 ◽  
Vol 5 (3) ◽  
pp. 141
Author(s):  
B. Murali Krishna ◽  
CH. Surendra ◽  
K. Mani Varma ◽  
K. Mani Kanta ◽  
S.K. Shabbeer ◽  
...  
Keyword(s):  
Dna Sequence ◽  
Dna Sequences ◽  
Deoxyribonucleic Acid ◽  
Specific Reference ◽  
Insertion Technique ◽  
Second Stage ◽  
Dna Cryptography ◽  
Single Strategy ◽  
Security Algorithm ◽  
Two Stages

<p>To convey the information safely DNA grouping mechanisms are used. There are many methods used by DNA sequences. The proposed method is of both encryption and information concealing utilizing a few properties of Deoxyribonucleic Acid (DNA) groupings. This technique is highlighted that DNA groupings have many more intriguing properties which are used for concealing the information. There are three strategies in this encryption strategy: the Insertion Technique, the Complimentary Pair Technique and the Substitution Strategy .For every single strategy, a specific reference DNA grouping P is chosen and then the taken sequence is changed over with the mystery message M and is consolidated, so that P0 is acquired. P0 is then sent to the collector and the beneficiary can recognize and separate the message M covered up in P. This technique is proposed to utilize INSERTION Strategy. Subsequently, the proposed plan comprises for the most part of two stages. In the principal stage, the mystery information is encoded utilizing a DNA Sequence. In the second stage the encoded information is steganographically covered up into some reference DNA grouping utilizing an insertion strategy. The effectiveness of this security algorithm is seen with many merits and limitations. A, C, G, and T are the 4 nucleotides which are taken for this project.</p>

Deoxyribonucleic acid methylation and chromatin organization in Tetrahymena thermophila

1981 ◽  
Vol 1 (7) ◽  
pp. 600-608
Author(s):  
K Pratt ◽  
S Hattman
Keyword(s):  
Dna Replication ◽  
Dna Sequence ◽  
Dna Sequences ◽  
Cytosine Methylation ◽  
Deoxyribonucleic Acid ◽  
Tetrahymena Thermophila ◽  
Staphylococcal Nuclease ◽  
Chromatin Organization ◽  
Deoxyribonuclease I ◽  
Cell Biol

Deoxyribonucleic acid (DNA) of the transcriptionally active macronucleus of Tetrahymena thermophila is methylated at the N6 position of adenine to produce methyladenine (MeAde); approximately 1 in every 125 adenine residues (0.8 mol%) is methylated. Transcriptionally inert micronuclear DNA is not methylated (< or = 0.01 mol% MeAde; M. A. Gorovsky, S. Hattman, and G. L. Pleger, J. Cell Biol. 56:697-701, 1973). There is no detectable cytosine methylation in macronuclei in Tetrahymena DNA (< or = 0.01 mol% 5-methylcytosine). MeAde-containing DNA sequences in macronuclei are preferentially digested by both staphylococcal nuclease and pancreatic deoxyribonuclease I. In contrast, there is no preferential release of MeAde during digestion of purified DNA. These results indicate that MeAde residues are predominantly located in "linker DNA" and perhaps have a function in transcription. Pulse-chase studies showed that labeled MeAde remains preferentially in linker DNA during subsequent rounds of DNA replication; i.e., there is little, if any, movement of nucleosomes during chromatin replication. This implies that nucleosomes may be phased with respect to DNA sequence.

scholarly journals SELF-SIMILARITY LIMITS OF GENOMIC SIGNATURES

Fractals ◽  
2003 ◽  
Vol 11 (01) ◽  
pp. 19-25 ◽  
Author(s):  
ZUO-BING WU
Keyword(s):  
Dna Sequence ◽  
Dna Sequences ◽  
Finite Sequence ◽  
Self Similarity ◽  
String Length ◽  
Chaos Game Representation ◽  
Genomic Signatures ◽  
Chaos Game ◽  
Representation Method ◽  
Complete Genomic

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 self-similarity limit in computing information dimension. By using the method, self-similarity limits of bacteria complete genomic signatures are further determined.

DNA sequence mapping in interphase and metaphase chromosomes by fluorescence in situ hybridization

1992 ◽  
Vol 50 (1) ◽  
pp. 496-497
Author(s):  
Barbara Trask ◽  
Susan Allen ◽  
Anne Bergmann ◽  
Mari Christensen ◽  
Anne Fertitta ◽  
...  
Keyword(s):  
In Situ Hybridization ◽  
Dna Sequence ◽  
Dna Sequences ◽  
Dual Band ◽  
Nick Translation ◽  
Metaphase Chromosomes ◽  
Band Pass ◽  
Texas Red ◽  
Fluorescent Spot

Using fluorescence in situ hybridization (FISH), the positions of DNA sequences can be discretely marked with a fluorescent spot. The efficiency of marking DNA sequences of the size cloned in cosmids is 90-95%, and the fluorescent spots produced after FISH are ≈0.3 μm in diameter. Sites of two sequences can be distinguished using two-color FISH. Different reporter molecules, such as biotin or digoxigenin, are incorporated into DNA sequence probes by nick translation. These reporter molecules are labeled after hybridization with different fluorochromes, e.g., FITC and Texas Red. The development of dual band pass filters (Chromatechnology) allows these fluorochromes to be photographed simultaneously without registration shift.

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