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Xrate
XRATE is a program for prototyping phylogenetic hidden Markov models and stochastic context-free grammars. It is used to discover patterns of evolutionary conservation in sequence alignments. The program can be used to estimate parameters for such models from "training" alignment data, or to apply the parameterized model so as to annotate new alignments. The program allows specification of a variety of models of DNA sequence evolution which may be arbitrarily organized using formal grammars. As an example of how XRATE is used, consider a protein-coding gene consisting of exons interspersed with introns. The exons contain triplets of nucleotides (codons) that are translated by ribosomes according to the genetic code, and consequently are under selection pressure (since any mutation may affect the translated amino acid sequence). In contrast, the introns are under fewer selective constraints and tend to evolve faster. These varying pressures show up clearly in multiple align ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Stockholm Format
Stockholm format is a multiple sequence alignment format used by Pfam, Rfam anDfam to disseminate protein, RNA and DNA sequence alignments. The alignment editorRaleehtml" ;"title=",;()[">,;()[aBb.-_--supports pseudoknot and further structure markup (see WUSS documentation) For protein [HGIEBTSCX] SA Surface Accessibility [0-9X] (0=0%-10%; ...; 9=90%-100%) TM TransMembrane [Mio] PP Posterior Probability [0-9*] (0=0.00-0.05; 1=0.05-0.15; *=0.95-1.00) LI LIgand binding AS Active Site pAS AS - Pfam predicted sAS AS - from SwissProt IN INtron (in or after) -2 For RNA tertiary interactions: ------------------------------ tWW WC/WC in trans For basepairs: />AaBb...Zz.html" ;"title=">AaBb...Zz">>AaBb...Zz For unpaired: cWH W ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Exons
An exon is any part of a gene that will form a part of the final mature RNA produced by that gene after introns have been removed by RNA splicing. The term ''exon'' refers to both the DNA sequence within a gene and to the corresponding sequence in RNA transcripts. In RNA splicing, introns are removed and exons are covalently joined to one another as part of generating the mature RNA. Just as the entire set of genes for a species constitutes the genome, the entire set of exons constitutes the exome. History The term ''exon'' derives from the expressed region and was coined by American biochemist Walter Gilbert in 1978: "The notion of the cistron… must be replaced by that of a transcription unit containing regions which will be lost from the mature messengerwhich I suggest we call introns (for intragenic regions)alternating with regions which will be expressedexons." This definition was originally made for protein-coding transcripts that are spliced before being translated. Th ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Continuous-time Markov Process
A continuous-time Markov chain (CTMC) is a continuous stochastic process in which, for each state, the process will change state according to an exponential random variable and then move to a different state as specified by the probabilities of a stochastic matrix. An equivalent formulation describes the process as changing state according to the least value of a set of exponential random variables, one for each possible state it can move to, with the parameters determined by the current state. An example of a CTMC with three states \ is as follows: the process makes a transition after the amount of time specified by the holding time—an exponential random variable E_i, where ''i'' is its current state. Each random variable is independent and such that E_0\sim \text(6), E_1\sim \text(12) and E_2\sim \text(18). When a transition is to be made, the process moves according to the jump chain, a discrete-time Markov chain with stochastic matrix: :\begin 0 & \frac & \frac \\ \frac & ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Formal Grammar
In formal language theory, a grammar (when the context is not given, often called a formal grammar for clarity) describes how to form strings from a language's alphabet that are valid according to the language's syntax. A grammar does not describe the meaning of the strings or what can be done with them in whatever context—only their form. A formal grammar is defined as a set of production rules for such strings in a formal language. Formal language theory, the discipline that studies formal grammars and languages, is a branch of applied mathematics. Its applications are found in theoretical computer science, theoretical linguistics, formal semantics, mathematical logic, and other areas. A formal grammar is a set of rules for rewriting strings, along with a "start symbol" from which rewriting starts. Therefore, a grammar is usually thought of as a language generator. However, it can also sometimes be used as the basis for a "recognizer"—a function in computing that deter ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Multiple Sequence Alignment
Multiple sequence alignment (MSA) may refer to the process or the result of sequence alignment of three or more biological sequences, generally protein, DNA, or RNA. In many cases, the input set of query sequences are assumed to have an evolutionary relationship by which they share a linkage and are descended from a common ancestor. From the resulting MSA, sequence homology can be inferred and phylogenetic analysis can be conducted to assess the sequences' shared evolutionary origins. Visual depictions of the alignment as in the image at right illustrate mutation events such as point mutations (single amino acid or nucleotide changes) that appear as differing characters in a single alignment column, and insertion or deletion mutations (indels or gaps) that appear as hyphens in one or more of the sequences in the alignment. Multiple sequence alignment is often used to assess sequence conservation of protein domains, tertiary and secondary structures, and even individual amino acid ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Amino Acid Sequence
Protein primary structure is the linear sequence of amino acids in a peptide or protein. By convention, the primary structure of a protein is reported starting from the amino-terminal (N) end to the carboxyl-terminal (C) end. Protein biosynthesis is most commonly performed by ribosomes in cells. Peptides can also be synthesized in the laboratory. Protein primary structures can be directly sequenced, or inferred from DNA sequences. Formation Biological Amino acids are polymerised via peptide bonds to form a long backbone, with the different amino acid side chains protruding along it. In biological systems, proteins are produced during translation by a cell's ribosomes. Some organisms can also make short peptides by non-ribosomal peptide synthesis, which often use amino acids other than the standard 20, and may be cyclised, modified and cross-linked. Chemical Peptides can be synthesised chemically via a range of laboratory methods. Chemical methods typically synthe ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Selection Pressure
Any cause that reduces or increases reproductive success in a portion of a population potentially exerts evolutionary pressure, selective pressure or selection pressure, driving natural selection. It is a quantitative description of the amount of change occurring in processes investigated by evolutionary biology, but the formal concept is often extended to other areas of research. In population genetics, selective pressure is usually expressed as a selection coefficient. Amino acids selective pressure It has been shown that putting an amino acid bio-synthesizing gene like ''HIS4'' gene under amino acid selective pressure in yeast causes enhancement of expression of adjacent genes which is due to the transcriptional co-regulation of two adjacent genes in Eukaryota. Antibiotic resistance Drug resistance in bacteria is an example of an outcome of natural selection. When a drug is used on a species of bacteria, those that cannot resist die and do not produce offspring, while tho ... [...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] |
Ribosomes
Ribosomes ( ) are macromolecular machines, found within all cells, that perform biological protein synthesis (mRNA translation). Ribosomes link amino acids together in the order specified by the codons of messenger RNA (mRNA) molecules to form polypeptide chains. Ribosomes consist of two major components: the small and large ribosomal subunits. Each subunit consists of one or more ribosomal RNA (rRNA) molecules and many ribosomal proteins (RPs or r-proteins). The ribosomes and associated molecules are also known as the ''translational apparatus''. Overview The sequence of DNA that encodes the sequence of the amino acids in a protein is transcribed into a messenger RNA chain. Ribosomes bind to messenger RNAs and use their sequences for determining the correct sequence of amino acids to generate a given protein. Amino acids are selected and carried to the ribosome by transfer RNA (tRNA) molecules, which enter the ribosome and bind to the messenger RNA chain via an anti-cod ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Codons
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 Efforts ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Introns
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 s ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
