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Horizontal Correlation
Horizontal correlation is a methodology for gene sequence analysis. Rather than referring to one specific technique, ''horizontal correlation'' instead encompasses a variety of approaches to sequence analysis that are unified by two specific themes: * Sequence analysis is performed by making comparisons ''horizontally'', along the length of a single genetic sequence; this is in contrast to ''vertical'' methods that make comparisons across several different genetic sequences. * The comparisons made generally measure information theoretic quantities such as value of the mutual information function between two regions of the sequence. The core ideas of the horizontal correlation approach were first presented in a year 2000 paper by Grosse, Herzel, Buldyrev, and Stanley (Grosse, et al. 2000). In this first formulation, Grosse and colleagues sought to characterize a large genetic sequence by dividing the sequence into coding and non-coding regions. Whereas traditional approaches to ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Gene
In biology, the word gene (from , ; "...Wilhelm Johannsen coined the word gene to describe the Mendelian units of heredity..." meaning ''generation'' or ''birth'' or ''gender'') can have several different meanings. The Mendelian gene is a basic unit of heredity and the molecular gene is a sequence of nucleotides in DNA that is transcribed to produce a functional RNA. There are two types of molecular genes: protein-coding genes and noncoding genes. During gene expression, the DNA is first copied into RNA. The RNA can be directly functional or be the intermediate template for a protein that performs a function. The transmission of genes to an organism's offspring is the basis of the inheritance of phenotypic traits. These genes make up different DNA sequences called genotypes. Genotypes along with environmental and developmental factors determine what the phenotypes will be. Most biological traits are under the influence of polygenes (many different genes) as well as gen ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Information Theory
Information theory is the scientific study of the quantification (science), quantification, computer data storage, storage, and telecommunication, communication of information. The field was originally established by the works of Harry Nyquist and Ralph Hartley, in the 1920s, and Claude Shannon in the 1940s. The field is at the intersection of probability theory, statistics, computer science, statistical mechanics, information engineering (field), information engineering, and electrical engineering. A key measure in information theory is information entropy, entropy. Entropy quantifies the amount of uncertainty involved in the value of a random variable or the outcome of a random process. For example, identifying the outcome of a fair coin flip (with two equally likely outcomes) provides less information (lower entropy) than specifying the outcome from a roll of a dice, die (with six equally likely outcomes). Some other important measures in information theory are mutual informat ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Mutual Information
In probability theory and information theory, the mutual information (MI) of two random variables is a measure of the mutual dependence between the two variables. More specifically, it quantifies the " amount of information" (in units such as shannons (bits), nats or hartleys) obtained about one random variable by observing the other random variable. The concept of mutual information is intimately linked to that of entropy of a random variable, a fundamental notion in information theory that quantifies the expected "amount of information" held in a random variable. Not limited to real-valued random variables and linear dependence like the correlation coefficient, MI is more general and determines how different the joint distribution of the pair (X,Y) is from the product of the marginal distributions of X and Y. MI is the expected value of the pointwise mutual information (PMI). The quantity was defined and analyzed by Claude Shannon in his landmark paper "A Mathemati ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Genetic Code
The genetic code is the set of rules used by living cells to translate information encoded within genetic material ( DNA or RNA sequences of nucleotide triplets, or codons) into proteins. Translation is accomplished by the ribosome, which links proteinogenic amino acids in an order specified by messenger RNA (mRNA), using transfer RNA (tRNA) molecules to carry amino acids and to read the mRNA three nucleotides at a time. The genetic code is highly similar among all organisms and can be expressed in a simple table with 64 entries. The codons specify which amino acid will be added next during protein biosynthesis. With some exceptions, a three-nucleotide codon in a nucleic acid sequence specifies a single amino acid. The vast majority of genes are encoded with a single scheme (see the RNA codon table). That scheme is often referred to as the canonical or standard genetic code, or simply ''the'' genetic code, though variant codes (such as in mitochondria) exist. History Effor ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Shotgun Sequencing
In genetics, shotgun sequencing is a method used for sequencing random DNA strands. It is named by analogy with the rapidly expanding, quasi-random shot grouping of a shotgun. The Sanger sequencing#Method, chain-termination method of DNA sequencing ("Sanger sequencing") can only be used for short DNA strands of 100 to 1000 base pairs. Due to this size limit, longer sequences are subdivided into smaller fragments that can be sequenced separately, and these sequences are sequence assembly, assembled to give the overall sequence. In shotgun sequencing, DNA is broken up randomly into numerous small segments, which are sequenced using the chain termination method to obtain ''reads''. Multiple overlapping reads for the target DNA are obtained by performing several rounds of this fragmentation and sequencing. Computer programs then use the overlapping ends of different reads to assemble them into a continuous sequence. Shotgun sequencing was one of the precursor technologies that was res ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
