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Some Notes on 2-D Graphical Representation of dna sequence

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Some Notes on 2-D Graphical Representation of DNA Sequence

ANIMAL TROPHOBLAST PROTEIN GENE-LIKE sequence OF HUMAN INTERFERON-ω1 GENE ISOLATED AND CLONED FROM CHINESE CHROMOSOME dna

第二十七届中国控制会议

作者： Liu Xikui,Li Yan College of Information&Engineering,Shandong University of Science and Technology,Qingdao 266510,P.R.China

Effective representation of long dna sequences has led to several innovative techniques to provide useful ways of viewing,sorting,analyzing,and comparing various *** 2-D and 3-D graphical representations of dna sequences have been given by Nandy,Leong and Mogenthaler,and Randic et al.,which give visual characterizations of dna sequences. In this paper,we presented a novel graphical representation of dna sequences by taking four special vectors in 2-D Cartesian coordinate system to represent the four nucleic acid bases in dna sequences,so that a dna sequence is denoted on a plane by a directed *** paper gives a example to illustrate the efficiemcy of the *** is shown that the new graphical representation of dna sequences has lower or nondegeneracy.

关键词： dna sequence Ggraphical rrepresentations Degeneracy

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Progress in Natural Science:Materials International 1992年第1期 74-76页

作者：黎孟枫郭辉玉侯云德 Department of Microbiology & Immunology Sun Yat-sen University of Medical Sciences. Guangzhou 510089 PRC. Department of Microbiology & Immunology Sun Yat-sen University of Medical Sciences. Guangzhou 510089 PRC. Institute of Virology Chinese Academy of Preventive Medicine. National Laboratory of Molecular Virology. Beijing 100052 PRC

Animal trophoblast proteins (TP) are a family of anti-luteolysins secreted bytrophectodermic cells during early pregnancy, acting specifically on endometrium. Amongthem genes of ovine trophoblast protein-1 (oTP-1)and bovine trophoblast protein-1 (bTP-1)were cloned and analyzed in Robert’s laboratory in 1987 and 1989, respectively. Fairly

关键词： trophoblast protein interferon dna polymerase chain reaction (PCR) dna sequence

LONG-RANGE CORRELATIONS IN dna sequenceS USING TWO-DIMENSIONAL dna WALKS

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Chinese Journal of Polymer Science 2005年第1期23卷 11-16页

作者： JinChena Lin-xiZhanga De-luZhaob DepartmentofPhysics WenzhouNormalCollegeWenzhou325027China PolymerPhysicsLaboratory CenterofMolecularScienceInstituteofChemistryChineseAcademyofSciencesBeijing100080China

The characterization of long-range correlations and fractal properties of dna sequences has proved to be adifficult though rewarding task mainly due to the mosaic character of dna consisting of many patches of various lengthswith different nucleotide *** this paper we investigate statistical correlations among different positions in dnasequences using the two-dimensional dna *** root-mean-square fluctuation F(l)is described by a power *** function C(l),which is used to measure the linear dependence and periodicity,exists a power law ofC(l)-l^(-μ).We also calculate the mean-square distancealong the dna chain,and it may be expressed as-l^(?)with 2>γ>*** investigations can provide some insights into long-range correlations in dna sequences.

关键词： Autocorrelation function dna sequence Long-range correlation.

Chaos game representation(CGR)-walk model for dna sequences

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Chinese Physics B 2009年第1期18卷 370-376页

作者：高洁徐振源 School of Science Jiangnan University School of Information Technology Jiangnan University

Chaos game representation （CGR） is an iterative mapping technique that processes sequences of units, such as nucleotides in a dna sequence or amino acids in a protein, in order to determine the coordinates of their positions in a continuous space. This distribution of positions has two features： one is unique, and the other is source sequence that can be recovered from the coordinates so that the distance between positions may serve as a measure of similarity between the corresponding sequences. A CGR-walk model is proposed based on CGR coordinates for the dna sequences. The CGR coordinates are converted into a time series, and a long-memory ARFIMA （p, d, q） model, where ARFIMA stands for autoregressive fractionally integrated moving average, is introduced into the dna sequence analysis. This model is applied to simulating real CGR-walk sequence data of ten genomic sequences. Remarkably long-range correlations are uncovered in the data, and the results from these models are reasonably fitted with those from the ARFIMA （p, d, q） model.

关键词： CGR-walk model dna sequence long-memory ARFIMA(p d q) model

Statistical properties of nucleotide clusters in dna sequences

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Journal of Zhejiang University-Science B(Biomedicine & Biotechnology) 2005年第5期6卷 408-412页

作者：成军章林溪 Department of Physics Jinhua University Jinhua 321017 China Department of Physics Zhejiang University Hangzhou 310027 China

Using the complete genome of Plasmodium falciparum 3D7 which has 14 chromosomes as an example, we have examined the distribution functions for the amount of C or G and A or T consecutively and non-overlapping blocks of m bases in this system. The function P(S) about the number of the consecutive C-G or A-T content cluster conforms to the relation P(S)∝e? ; αs values of the scaling exponent αCG are much larger than αAT; and αAT of 14 chromosomes are hardly changed, whereas αCG of 14 chromosomes have a number of fluctuations. We found maximum value of A-T cluster size is much larger than C-G, which implies the existence of large A-T cluster. Our study of the width function ξ(m) of cluster C-G content showed that follows good power law ξ(m)∝m?γ. The average γ for 14 chromosomes is 0.931. These investigations provide some insight into the nucleotide clusters of dna sequences, and help us understand other properties of dna sequences.

关键词： dna sequence Plasmodium falciparum 3D7 Nucleotide clusters Power law

Prediction of dna sequences using adaptative neuro-fuzzy inference system

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International Journal of Biomathematics 2018年第4期11卷 19-56页

作者： Assia Mihi Nourredine Boucenna Kheir Benmahammmed Faculty of Engineering Mohammed Kheider University Avenue Sidi Okba Biskra Algeria Department of Electronics Faculty of Engineering Mohamed El Bachir El Ibrahimi University Bordj Bou Arrdridj El Annasser Algeria Department of Electronics Faculty of EngineeringFerhat Abesse University El maabouda Setif Algeria

Accurate prediction and detection of the dna regions or their underlying structural patterns are constant difficulties for researchers. Feature extraction and functional classification of genomic sequences is an interesting area of research. Many computational techniques have already been applied including the artificial neural network （ANN）, nonlinear model, spectrogram and statistical techniques. In this paper, some features are extracted from the wavelet coefficient and second set of features are extracted from the frequency of transition of nucleotides. These two features sets are examined. The purpose was to investigate the abilities of these parameters to predict critical segment in the dna sequence. The neuro-fuzzy system was used for prediction. The performance of the neuro-fuzzy system was evaluated in terms of training performance and prediction accuracies. Two genomic sequences of the classes： prokaryotic and eukaryotic were used, as an example, （Escherichia coli） and （Caenorhabditis elegans） sequences were selected.

关键词： dna sequence adaptative neuro-fuzzy inference system(ANFIS) fuzzy logic wavelet transform genomic signal.

The number of alignments between two dna sequences

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International Journal of Biomathematics 2016年第4期9卷 75-80页

作者： Helena Andrade Juan J. Nieto Angela Torres Departamento de Andlisis Matemdtico Facultad de Matemdticas Universidad de Santiago de Compostela Spain Department of Mathematics Faculty of ScienceKing Abdulaziz University Jeddah 21589 Saudi Arabia Departamento de Psiquiatrla Radiologla y Salud Publica Facultad de Medicina Universidad de Santiago de Compostela Spain

We consider two dna sequences and compare both sequences. One of the crucial issues in bioinformatics is to measure the similarity of two dna sequences. To this purpose one has to consider different alignments between both sequences. The number of alignments grows very rapidly with the length of the sequences. In this paper we give exact, explicit and computable formulas for the number of different possible alignments and for some classes of reduced alignments. We provide a new insight into the theory of dna sequence alignment.

关键词： dna sequence alignment difference equation.

Using dna sequences and Phylogenetic Trees as Tools for Teaching Entomology to Undergraduate Students: A Simple Approach

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Advances in Entomology 2021年第4期9卷 147-154页

作者： Mohammad Ali Al-Deeb Biology Department United Arab Emirates University Al Ain UAE

This technical note aims to show how any instructor teaching entomology can use the Basic Local Alignment Search Tool (BLAST) and the “one click” mode of *** to teach undergraduate students about insect dna similarity in a simple way. Teaching an entomology course requires the use of numerous tools to help students grasp different concepts. Knowing that there are more than one million described species of insects means that teaching students about insect identification and taxonomy can be challenging. However, here we present two easy exercises that could be used as classroom or take-home assignments to demonstrate various levels of DNA similarity among different insect taxa. Such exercises unlock students’ creativity and break the barrier of fear of bioinformatics. Moreover, they open up new ways for them to understand insect taxonomy through molecular biology and allow them to develop new skills that contribute to strengthening their scientific performance in the future, especially when they do research as graduate students. Finally, this note is an example of how to integrate simple bioinformatics tools into the teaching of entomology.

关键词： dna sequence Phylogenetic Tree GenBank Teaching Entomology

dna Polymorphism Among Yewei B, V20B, and Oryza minuta J. S. Presl. ex C. B. Presl.

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Journal of Integrative Plant Biology 2005年第12期47卷 1485-1492页

作者： Bing-Ran ZHAO Quan-Hua XING Hong-Ai XIA He-Hua YANG De-Min JIN Xia LIU Song-Wen WANG Bin WANG Long-Ping YUAN China National Hybrid Rice R ＆ D Center Changsha 410125 China Institute of Genetics and Developmental Biology the Chinese Academy of Sciences Beijing 100010 China Tianjin Agriculture College Tianjin 300384 China

The new cytoplasmic male sterile （CMS） line Yewei A and its maintainer line Yewei B, with better agronomic characteristics, have been developed from a mutant of V20B （a rice maintainer line） through transformation of genomic dna of wild rice （Oryza minuta J. S. Presl. ex C. B. Presl.）. Analysis of molecular markers, dna sequences, and Southern blot revealed that high dna polymorphism exists between the mutant and its receptor, indicating that the special dna fragment from O. minuta may be integrated into the genome of Yewei B. Therefore, transformation of genomic dna from distant relatives to the plant of a target receptor may open an avenue for creating a new rice germplasm.

关键词： dna sequence genomic dna introduction germplasm molecular markers wild rice.