|
Hirschberg's Algorithm
In computer science, Hirschberg's algorithm, named after its inventor, Dan Hirschberg, is a dynamic programming algorithm that finds the optimal sequence alignment between two strings. Optimality is measured with the Levenshtein distance, defined to be the sum of the costs of insertions, replacements, deletions, and null actions needed to change one string into the other. Hirschberg's algorithm is simply described as a more space-efficient version of the Needleman–Wunsch algorithm that uses divide and conquer. Hirschberg's algorithm is commonly used in computational biology to find maximal global alignments of DNA and protein sequences. Algorithm information Hirschberg's algorithm is a generally applicable algorithm for optimal sequence alignment. BLAST and FASTA are suboptimal heuristics. If ''x'' and ''y'' are strings, where length(''x'') = ''n'' and length(''y'') = ''m'', the Needleman–Wunsch algorithm finds an optimal alignment in O(''nm'') time, using O(''nm'') space. ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Computer Science
Computer science is the study of computation, automation, and information. Computer science spans theoretical disciplines (such as algorithms, theory of computation, information theory, and automation) to Applied science, practical disciplines (including the design and implementation of Computer architecture, hardware and Computer programming, software). Computer science is generally considered an area of research, academic research and distinct from computer programming. Algorithms and data structures are central to computer science. The theory of computation concerns abstract models of computation and general classes of computational problem, problems that can be solved using them. The fields of cryptography and computer security involve studying the means for secure communication and for preventing Vulnerability (computing), security vulnerabilities. Computer graphics (computer science), Computer graphics and computational geometry address the generation of images. Progr ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
FASTA
FASTA is a DNA and protein sequence alignment software package first described by David J. Lipman and William R. Pearson in 1985. Its legacy is the FASTA format which is now ubiquitous in bioinformatics. History The original FASTA program was designed for protein sequence similarity searching. Because of the exponentially expanding genetic information and the limited speed and memory of computers in the 1980s heuristic methods were introduced aligning a query sequence to entire data-bases. FASTA, published in 1987, added the ability to do DNA:DNA searches, translated protein:DNA searches, and also provided a more sophisticated shuffling program for evaluating statistical significance. There are several programs in this package that allow the alignment of protein sequences and DNA sequences. Nowadays, increased computer performance makes it possible to perform searches for local alignment detection in a database using the Smith–Waterman algorithm. FASTA is pronounced "fas ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Bioinformatics Algorithms
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 ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Sequence Alignment Algorithms
In mathematics, a sequence is an enumerated collection of objects in which repetitions are allowed and order matters. Like a set, it contains members (also called ''elements'', or ''terms''). The number of elements (possibly infinite) is called the ''length'' of the sequence. Unlike a set, the same elements can appear multiple times at different positions in a sequence, and unlike a set, the order does matter. Formally, a sequence can be defined as a function from natural numbers (the positions of elements in the sequence) to the elements at each position. The notion of a sequence can be generalized to an indexed family, defined as a function from an ''arbitrary'' index set. For example, (M, A, R, Y) is a sequence of letters with the letter 'M' first and 'Y' last. This sequence differs from (A, R, M, Y). Also, the sequence (1, 1, 2, 3, 5, 8), which contains the number 1 at two different positions, is a valid sequence. Sequences can be ''finite'', as in these examples, or ''infinite ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Longest Common Subsequence Problem
The longest common subsequence (LCS) problem is the problem of finding the longest subsequence common to all sequences in a set of sequences (often just two sequences). It differs from the longest common substring problem: unlike substrings, subsequences are not required to occupy consecutive positions within the original sequences. The longest common subsequence problem is a classic computer science problem, the basis of data comparison programs such as the diff utility, and has applications in computational linguistics and bioinformatics. It is also widely used by revision control systems such as Git for reconciling multiple changes made to a revision-controlled collection of files. For example, consider the sequences (ABCD) and (ACBAD). They have 5 length-2 common subsequences: (AB), (AC), (AD), (BD), and (CD); 2 length-3 common subsequences: (ABD) and (ACD); and no longer common subsequences. So (ABD) and (ACD) are their longest common subsequences. Complexity For the ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Arg Max
In mathematics, the arguments of the maxima (abbreviated arg max or argmax) are the points, or elements, of the domain of some function at which the function values are maximized.For clarity, we refer to the input (''x'') as ''points'' and the output (''y'') as ''values;'' compare critical point and critical value. In contrast to global maxima, which refers to the largest ''outputs'' of a function, arg max refers to the ''inputs'', or arguments, at which the function outputs are as large as possible. Definition Given an arbitrary set a totally ordered set and a function, the \operatorname over some subset S of X is defined by :\operatorname_S f := \underset\, f(x) := \. If S = X or S is clear from the context, then S is often left out, as in \underset\, f(x) := \. In other words, \operatorname is the set of points x for which f(x) attains the function's largest value (if it exists). \operatorname may be the empty set, a singleton, or contain multiple elements. In th ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Communications Of The ACM
''Communications of the ACM'' is the monthly journal of the Association for Computing Machinery (ACM). It was established in 1958, with Saul Rosen as its first managing editor. It is sent to all ACM members. Articles are intended for readers with backgrounds in all areas of computer science and information systems. The focus is on the practical implications of advances in information technology and associated management issues; ACM also publishes a variety of more theoretical journals. The magazine straddles the boundary of a science magazine, trade magazine, and a scientific journal. While the content is subject to peer review, the articles published are often summaries of research that may also be published elsewhere. Material published must be accessible and relevant to a broad readership. From 1960 onward, ''CACM'' also published algorithms, expressed in ALGOL. The collection of algorithms later became known as the Collected Algorithms of the ACM. See also * ''Journal of the A ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Diff
In computing, the utility diff is a data comparison tool that computes and displays the differences between the contents of files. Unlike edit distance notions used for other purposes, diff is line-oriented rather than character-oriented, but it is like Levenshtein distance in that it tries to determine the smallest set of deletions and insertions to create one file from the other. The utility displays the changes in one of several standard formats, such that both humans or computers can parse the changes, and use them for patching. Typically, ''diff'' is used to show the changes between two versions of the same file. Modern implementations also support binary files. The output is called a "diff", or a patch, since the output can be applied with the Unix program . The output of similar file comparison utilities is also called a "diff"; like the use of the word "grep" for describing the act of searching, the word ''diff'' became a generic term for calculating data difference and ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Longest Common Subsequence Problem
The longest common subsequence (LCS) problem is the problem of finding the longest subsequence common to all sequences in a set of sequences (often just two sequences). It differs from the longest common substring problem: unlike substrings, subsequences are not required to occupy consecutive positions within the original sequences. The longest common subsequence problem is a classic computer science problem, the basis of data comparison programs such as the diff utility, and has applications in computational linguistics and bioinformatics. It is also widely used by revision control systems such as Git for reconciling multiple changes made to a revision-controlled collection of files. For example, consider the sequences (ABCD) and (ACBAD). They have 5 length-2 common subsequences: (AB), (AC), (AD), (BD), and (CD); 2 length-3 common subsequences: (ABD) and (ACD); and no longer common subsequences. So (ABD) and (ACD) are their longest common subsequences. Complexity For the ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Big O Notation
Big ''O'' notation is a mathematical notation that describes the limiting behavior of a function when the argument tends towards a particular value or infinity. Big O is a member of a family of notations invented by Paul Bachmann, Edmund Landau, and others, collectively called Bachmann–Landau notation or asymptotic notation. The letter O was chosen by Bachmann to stand for ''Ordnung'', meaning the order of approximation. In computer science, big O notation is used to classify algorithms according to how their run time or space requirements grow as the input size grows. In analytic number theory, big O notation is often used to express a bound on the difference between an arithmetical function and a better understood approximation; a famous example of such a difference is the remainder term in the prime number theorem. Big O notation is also used in many other fields to provide similar estimates. Big O notation characterizes functions according to their growth rates: d ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Heuristic (computer Science)
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] |
BLAST
Blast or The Blast may refer to: * Explosion, a rapid increase in volume and release of energy in an extreme manner *Detonation, an exothermic front accelerating through a medium that eventually drives a shock front Film * ''Blast'' (1997 film), starring Andrew Divoff * ''Blast'' (2000 film), starring Liesel Matthews * ''Blast'' (2004 film), an action comedy film * ''Blast!'' (1972 film) or ''The Final Comedown'', an American drama * ''BLAST!'' (2008 film), a documentary about the BLAST telescope * '' A Blast'', a 2014 film directed by Syllas Tzoumerkas Magazines * ''Blast'' (magazine), a 1914–15 literary magazine of the Vorticist movement * ''Blast'' (U.S. magazine), a 1933–34 American short-story magazine * ''The Blast'' (magazine), a 1916–17 American anarchist periodical Music * Blast (American band), a hardcore punk band * Blast (Russian band), an indie band * ''Blast'' (album), by Holly Johnson, 1989 * ''The Blast'' (album), by Yuvan Shankar Raja, 1999 * " ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
