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Z-curve
The Z curve (or Z-curve) method is a bioinformatics algorithm for genome analysis. The Z-curve is a three-dimensional curve that constitutes a unique representation of a DNA sequence, i.e., for the Z-curve and the given DNA sequence each can be uniquely reconstructed from the other. The resulting curve has a zigzag shape, hence the name Z-curve. Background The Z Curve method was first created in 1994 as a way to visually map a DNA or RNA sequence. Different properties of the Z curve, such as its symmetry and periodicity can give unique information on the DNA sequence. The Z curve is generated from a series of nodes, P0, P1,...PN, with the coordinates xn, yn, and zn (n=0,1,2...N, with N being the length of the DNA sequence). The Z curve is created by connecting each of the nodes sequentially. x_ = (A_ + G_) - (C_ + T_) y_ = (A_ + C_) - (G_ + T_) z_ = (A_ + T_) - (C_ + G_) n = 0, 1, 2, ... N Applications Information on the distribution of nucleotides in a DNA sequence ca ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Gene Prediction
In computational biology, gene prediction or gene finding refers to the process of identifying the regions of genomic DNA that encode genes. This includes protein-coding genes as well as RNA genes, but may also include prediction of other functional elements such as regulatory regions. Gene finding is one of the first and most important steps in understanding the genome of a species once it has been sequenced. In its earliest days, "gene finding" was based on painstaking experimentation on living cells and organisms. Statistical analysis of the rates of homologous recombination of several different genes could determine their order on a certain chromosome, and information from many such experiments could be combined to create a genetic map specifying the rough location of known genes relative to each other. Today, with comprehensive genome sequence and powerful computational resources at the disposal of the research community, gene finding has been redefined as a largely computatio ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Z Curve Of C
Z (or z) is the 26th and last letter of the Latin alphabet, used in the modern English alphabet, the alphabets of other western European languages and others worldwide. Its usual names in English are ''zed'' () and ''zee'' (), with an occasional archaic variant ''izzard'' ()."Z", ''Oxford English Dictionary,'' 2nd edition (1989); ''Merriam-Webster's Third New International Dictionary of the English Language, Unabridged'' (1993); "zee", ''op. cit''. Name and pronunciation In most English-speaking countries, including Australia, Canada, India, Ireland, New Zealand and the United Kingdom, the letter's name is ''zed'' , reflecting its derivation from the Greek ''zeta'' (this dates to Latin, which borrowed Y and Z from Greek), but in American English its name is ''zee'' , analogous to the names for B, C, D, etc., and deriving from a late 17th-century English dialectal form. Another English dialectal form is ''izzard'' . This dates from the mid-18th century and probably derives fr ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Hydrogen Bond
In chemistry, a hydrogen bond (or H-bond) is a primarily electrostatic force of attraction between a hydrogen (H) atom which is covalently bound to a more electronegative "donor" atom or group (Dn), and another electronegative atom bearing a lone pair of electrons—the hydrogen bond acceptor (Ac). Such an interacting system is generally denoted , where the solid line denotes a polar covalent bond, and the dotted or dashed line indicates the hydrogen bond. The most frequent donor and acceptor atoms are the second-row elements nitrogen (N), oxygen (O), and fluorine (F). Hydrogen bonds can be intermolecular (occurring between separate molecules) or intramolecular (occurring among parts of the same molecule). The energy of a hydrogen bond depends on the geometry, the environment, and the nature of the specific donor and acceptor atoms and can vary between 1 and 40 kcal/mol. This makes them somewhat stronger than a van der Waals interaction, and weaker than fully covalent ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Intron
An intron is any nucleotide sequence within a gene that is not expressed or operative in the final RNA product. The word ''intron'' is derived from the term ''intragenic region'', i.e. a region inside a gene."The notion of the cistron .e., gene... must be replaced by that of a transcription unit containing regions which will be lost from the mature messenger – which I suggest we call introns (for intragenic regions) – alternating with regions which will be expressed – exons." (Gilbert 1978) The term ''intron'' refers to both the DNA sequence within a gene and the corresponding RNA sequence in RNA transcripts. The non-intron sequences that become joined by this RNA processing to form the mature RNA are called exons. Introns are found in the genes of most organisms and many viruses and they can be located in both protein-coding genes and genes that function as RNA (noncoding genes). There are four main types of introns: tRNA introns, group I introns, group II introns, and ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Comparative Genomics
Comparative genomics is a field of biological research in which the genomic features of different organisms are compared. The genomic features may include the DNA sequence, genes, gene order, regulatory sequences, and other genomic structural landmarks. In this branch of genomics, whole or large parts of genomes resulting from genome projects are compared to study basic biological similarities and differences as well as evolutionary relationships between organisms. The major principle of comparative genomics is that common features of two organisms will often be encoded within the DNA that is evolutionarily conserved between them. Therefore, comparative genomic approaches start with making some form of alignment of genome sequences and looking for orthologous sequences (sequences that share a common ancestry) in the aligned genomes and checking to what extent those sequences are conserved. Based on these, genome and molecular evolution are inferred and this may in turn be put in ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Genomic Island
A genomic island (GI) is part of a genome that has evidence of horizontal origins. The term is usually used in microbiology, especially with regard to bacteria. A GI can code for many functions, can be involved in symbiosis or pathogenesis, and may help an organism's adaptation. Many sub-classes of GIs exist that are based on the function that they confer. For example, a GI associated with pathogenesis is often called a pathogenicity island (PAIs), while GIs that contain many antibiotic resistant genes are referred to as antibiotic resistance islands. The same GI can occur in distantly related species as a result of various types of lateral gene transfer (transformation, conjugation, transduction). This can be determined by base composition analysis, as well as phylogeny estimations. Computational prediction Various genomic island predictions programs have been developed. These tools can be broadly grouped into sequence based methods and comparative genomics/phylogeny based ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Isochore (genetics)
In genetics, an isochore is a large region of genomic DNA (greater than 300 kilobases) with a high degree of uniformity in GC content; that is, guanine (G) and cytosine (C) bases. The distribution of bases within a genome is non-random: different regions of the genome have different amounts of G-C base pairs, such that regions can be classified and identified by the proportion of G-C base pairs they contain. Bernardi and colleagues first noticed the compositional non-uniformity of vertebrate genomes using thermal melting and density gradient centrifugation. The DNA fragments extracted by the gradient centrifugation were later termed "isochores", which was subsequently defined as "very long (much greater than 200 KB) DNA segments" that "are fairly homogeneous in base composition and belong to a small number of major classes distinguished by differences in guanine-cytosine (GC) content". Subsequently, the isochores "grew" and were claimed to be ">300 kb in size." The theory propos ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Nucleic Acids Research
''Nucleic Acids Research'' is an open-access peer-reviewed scientific journal published since 1974 by the Oxford University Press. The journal covers research on nucleic acids, such as DNA and RNA, and related work. According to the ''Journal Citation Reports'', the journal's 2021 impact factor is 19.160. The journal publishes two yearly special issues, the first issue of each year is dedicated to biological databases, published in January since 1993, and the other is devoted to papers describing web-based software resources of value to the biological community (web server A web server is computer software and underlying hardware that accepts requests via HTTP (the network protocol created to distribute web content) or its secure variant HTTPS. A user agent, commonly a web browser or web crawler, initiate ...s), published in July since 2003. References External links * * Archives , https://www.ncbi.nlm.nih.gov/pmc/journals/4/ Biochemistry journals Open access j ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Replication Origin
The origin of replication (also called the replication origin) is a particular sequence in a genome at which replication is initiated. Propagation of the genetic material between generations requires timely and accurate duplication of DNA by semiconservative replication prior to cell division to ensure each daughter cell receives the full complement of chromosomes. Material was copied from this source, which is available under Creative Commons Attribution 4.0 International License This can either involve the replication of DNA in living organisms such as prokaryotes and eukaryotes, or that of DNA or RNA in viruses, such as double-stranded RNA viruses. Synthesis of daughter strands starts at discrete sites, termed replication origins, and proceeds in a bidirectional manner until all genomic DNA is replicated. Despite the fundamental nature of these events, organisms have evolved surprisingly divergent strategies that control replication onset. Although the specific replication or ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Pyrimidine
Pyrimidine (; ) is an aromatic, heterocyclic, organic compound similar to pyridine (). One of the three diazines (six-membered heterocyclics with two nitrogen atoms in the ring), it has nitrogen atoms at positions 1 and 3 in the ring. The other diazines are pyrazine (nitrogen atoms at the 1 and 4 positions) and pyridazine (nitrogen atoms at the 1 and 2 positions). In nucleic acids, three types of nucleobases are pyrimidine derivatives: cytosine (C), thymine (T), and uracil (U). Occurrence and history The pyrimidine ring system has wide occurrence in nature as substituted and ring fused compounds and derivatives, including the nucleotides cytosine, thymine and uracil, thiamine (vitamin B1) and alloxan. It is also found in many synthetic compounds such as barbiturates and the HIV drug, zidovudine. Although pyrimidine derivatives such as alloxan were known in the early 19th century, a laboratory synthesis of a pyrimidine was not carried out until 1879, when Grimaux reported the ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Bioinformatics
Bioinformatics () is an interdisciplinary field that develops methods and software tools for understanding biological data, in particular when the data sets are large and complex. As an interdisciplinary field of science, bioinformatics combines biology, chemistry, physics, computer science, information engineering, mathematics and statistics to analyze and interpret the biological data. Bioinformatics has been used for '' in silico'' analyses of biological queries using computational and statistical techniques. Bioinformatics includes biological studies that use computer programming as part of their methodology, as well as specific analysis "pipelines" that are repeatedly used, particularly in the field of genomics. Common uses of bioinformatics include the identification of candidates genes and single nucleotide polymorphisms (SNPs). Often, such identification is made with the aim to better understand the genetic basis of disease, unique adaptations, desirable properties (e ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Purine
Purine is a heterocyclic compound, heterocyclic aromatic organic compound that consists of two rings (pyrimidine and imidazole) fused together. It is water-soluble. Purine also gives its name to the wider class of molecules, purines, which include substituted purines and their tautomers. They are the most widely occurring nitrogen-containing heterocycles in nature. Dietary sources Purines are found in high concentration in meat and meat products, especially internal organs such as liver and kidney. In general, plant-based diets are low in purines. High-purine plants and algae include some legumes (lentils and Black-eyed pea, black eye peas) and Spirulina (dietary supplement), spirulina. Examples of high-purine sources include: sweetbreads, Anchovies as food, anchovies, Sardines as food, sardines, liver, beef kidneys, Brain as food, brains, meat extracts (e.g., Oxo (food), Oxo, Bovril), herring, mackerel, scallops, game meats, yeast (beer, yeast extract, nutritional yeast) and g ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
