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Tree Alignment
In computational phylogenetics, tree alignment is a computational problem concerned with producing multiple sequence alignments, or alignments of three or more sequences of DNA, RNA, or protein. Sequences are arranged into a phylogenetic tree, modeling the evolutionary relationships between species or taxa. The edit distances between sequences are calculated for each of the tree's internal vertices, such that the sum of all edit distances within the tree is minimized. Tree alignment can be accomplished using one of several algorithms with various trade-offs between manageable tree size and computational effort. Definition Input: A set S of sequences, a phylogenetic tree T leaf-labeled by S and an edit distance function d between sequences. Output: A labeling of the internal vertices of T such that \Sigma_ d(e) is minimized, where d(e) is the edit distance between the endpoints of e. The task is NP-hard. Background Sequence alignment In bioinformatics, the basic method of info ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Computational Phylogenetics
Computational phylogenetics is the application of computational algorithms, methods, and programs to phylogenetic"origin,_source,_birth")_is_the_study_of_the_evolutionary_his_... "origin, source, birth") is the study of the evolutionary his ... "origin, source, birth") is the study of the evolutionary his ... "origin, source, birth") is the study of the evolutionary his ... "origin, source, birth") is the study of the evolutionary his ... "tribe, clan, race", and wikt:γενετικός, γενετικός [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
NP-complete
In computational complexity theory, a problem is NP-complete when: # it is a problem for which the correctness of each solution can be verified quickly (namely, in polynomial time) and a brute-force search algorithm can find a solution by trying all possible solutions. # the problem can be used to simulate every other problem for which we can verify quickly that a solution is correct. In this sense, NP-complete problems are the hardest of the problems to which solutions can be verified quickly. If we could find solutions of some NP-complete problem quickly, we could quickly find the solutions of every other problem to which a given solution can be easily verified. The name "NP-complete" is short for "nondeterministic polynomial-time complete". In this name, "nondeterministic" refers to nondeterministic Turing machines, a way of mathematically formalizing the idea of a brute-force search algorithm. Polynomial time refers to an amount of time that is considered "quick" for a de ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
A* Search Algorithm
A* (pronounced "A-star") is a graph traversal and path search algorithm, which is used in many fields of computer science due to its completeness, optimality, and optimal efficiency. One major practical drawback is its O(b^d) space complexity, as it stores all generated nodes in memory. Thus, in practical travel-routing systems, it is generally outperformed by algorithms which can pre-process the graph to attain better performance, as well as memory-bounded approaches; however, A* is still the best solution in many cases. Peter Hart, Nils Nilsson and Bertram Raphael of Stanford Research Institute (now SRI International) first published the algorithm in 1968. It can be seen as an extension of Dijkstra's algorithm. A* achieves better performance by using heuristics to guide its search. Compared to Dijkstra's algorithm, the A* algorithm only finds the shortest path from a specified source to a specified goal, and not the shortest-path tree from a specified source to all possi ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Iterative
Iteration is the repetition of a process in order to generate a (possibly unbounded) sequence of outcomes. Each repetition of the process is a single iteration, and the outcome of each iteration is then the starting point of the next iteration. In mathematics and computer science, iteration (along with the related technique of recursion) is a standard element of algorithms. Mathematics In mathematics, iteration may refer to the process of iterating a function, i.e. applying a function repeatedly, using the output from one iteration as the input to the next. Iteration of apparently simple functions can produce complex behaviors and difficult problems – for examples, see the Collatz conjecture and juggler sequences. Another use of iteration in mathematics is in iterative methods which are used to produce approximate numerical solutions to certain mathematical problems. Newton's method is an example of an iterative method. Manual calculation of a number's square root is a co ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Heuristic Algorithm
In mathematical optimization and computer science, heuristic (from Greek εὑρίσκω "I find, discover") is a technique designed for solving a problem more quickly when classic methods are too slow for finding an approximate solution, or when classic methods fail to find any exact solution. This is achieved by trading optimality, completeness, accuracy, or precision for speed. In a way, it can be considered a shortcut. A heuristic function, also simply called a heuristic, is a function that ranks alternatives in search algorithms at each branching step based on available information to decide which branch to follow. For example, it may approximate the exact solution. Definition and motivation The objective of a heuristic is to produce a solution in a reasonable time frame that is good enough for solving the problem at hand. This solution may not be the best of all the solutions to this problem, or it may simply approximate the exact solution. But it is still valuable b ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Combinatorial Game Theory
Combinatorial game theory is a branch of mathematics and theoretical computer science that typically studies sequential games with perfect information. Study has been largely confined to two-player games that have a ''position'' that the players take turns changing in defined ways or ''moves'' to achieve a defined winning condition. Combinatorial game theory has not traditionally studied games of chance or those that use imperfect or incomplete information, favoring games that offer perfect information in which the state of the game and the set of available moves is always known by both players. However, as mathematical techniques advance, the types of game that can be mathematically analyzed expands, thus the boundaries of the field are ever changing. Scholars will generally define what they mean by a "game" at the beginning of a paper, and these definitions often vary as they are specific to the game being analyzed and are not meant to represent the entire scope of the field. C ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Evolutionary Tree
A phylogenetic tree (also phylogeny or evolutionary tree Felsenstein J. (2004). ''Inferring Phylogenies'' Sinauer Associates: Sunderland, MA.) is a branching diagram or a tree showing the evolutionary relationships among various biological species or other entities based upon similarities and differences in their physical or genetic characteristics. All life on Earth is part of a single phylogenetic tree, indicating common ancestry. In a ''rooted'' phylogenetic tree, each node with descendants represents the inferred most recent common ancestor of those descendants, and the edge lengths in some trees may be interpreted as time estimates. Each node is called a taxonomic unit. Internal nodes are generally called hypothetical taxonomic units, as they cannot be directly observed. Trees are useful in fields of biology such as bioinformatics, systematics, and phylogenetics. ''Unrooted'' trees illustrate only the relatedness of the leaf nodes and do not require the ancestral root to ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Combinatorial Optimization
Combinatorial optimization is a subfield of mathematical optimization that consists of finding an optimal object from a finite set of objects, where the set of feasible solutions is discrete or can be reduced to a discrete set. Typical combinatorial optimization problems are the travelling salesman problem ("TSP"), the minimum spanning tree problem ("MST"), and the knapsack problem. In many such problems, such as the ones previously mentioned, exhaustive search is not tractable, and so specialized algorithms that quickly rule out large parts of the search space or approximation algorithms must be resorted to instead. Combinatorial optimization is related to operations research, algorithm theory, and computational complexity theory. It has important applications in several fields, including artificial intelligence, machine learning, auction theory, software engineering, VLSI, applied mathematics and theoretical computer science. Some research literature considers discrete o ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Exponential
Exponential may refer to any of several mathematical topics related to exponentiation, including: *Exponential function, also: **Matrix exponential, the matrix analogue to the above * Exponential decay, decrease at a rate proportional to value *Exponential discounting, a specific form of the discount function, used in the analysis of choice over time *Exponential growth, where the growth rate of a mathematical function is proportional to the function's current value *Exponential map (Riemannian geometry), in Riemannian geometry * Exponential map (Lie theory), in Lie theory * Exponential notation, also known as scientific notation, or standard form *Exponential object, in category theory *Exponential time, in complexity theory *in probability and statistics: ** Exponential distribution, a family of continuous probability distributions **Exponentially modified Gaussian distribution, describes the sum of independent normal and exponential random variables **Exponential family, a paramet ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Computational Biology
Computational biology refers to the use of data analysis, mathematical modeling and computational simulations to understand biological systems and relationships. An intersection of computer science, biology, and big data, the field also has foundations in applied mathematics, chemistry, and genetics. It differs from biological computing, a subfield of computer engineering which uses bioengineering to build computers. History Bioinformatics, the analysis of informatics processes in biological systems, began in the early 1970s. At this time, research in artificial intelligence was using network models of the human brain in order to generate new algorithms. This use of biological data pushed biological researchers to use computers to evaluate and compare large data sets in their own field. By 1982, researchers shared information via punch cards. The amount of data grew exponentially by the end of the 1980s, requiring new computational methods for quickly interpreting ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Base-pair Substitution
A point mutation is a genetic mutation where a single nucleotide base is changed, inserted or deleted from a DNA or RNA sequence of an organism's genome. Point mutations have a variety of effects on the downstream protein product—consequences that are moderately predictable based upon the specifics of the mutation. These consequences can range from no effect (e.g. synonymous mutations) to deleterious effects (e.g. frameshift mutations), with regard to protein production, composition, and function. Causes Point mutations usually take place during DNA replication. DNA replication occurs when one double-stranded DNA molecule creates two single strands of DNA, each of which is a template for the creation of the complementary strand. A single point mutation can change the whole DNA sequence. Changing one purine or pyrimidine may change the amino acid that the nucleotides code for. Point mutations may arise from spontaneous mutations that occur during DNA replication. The rate ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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