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Compressed Suffix Array
In computer science, a compressed suffix arrayR. Grossi and J. S. Vitter, Compressed Suffix Arrays and Suffix Trees, with Applications to Text Indexing and String Matching, ''SIAM Journal on Computing,'' 35(2), 2005, 378-407. An earlier version appeared in ''Proceedings of the 32nd ACM Symposium on Theory of Computing,'' May 2000, 397-406.Paolo Ferragina and Giovanni Manzini (2000). "Opportunistic Data Structures with Applications". Proceedings of the 41st Annual Symposium on Foundations of Computer Science. p.390.R. Grossi, A. Gupta, and J. S. Vitter, High-Order Entropy-Compressed Text Indexes, ''Proceedings of the 14th Annual SIAM/ACM Symposium on Discrete Algorithms,'' January 2003, 841-850. is a compressed data structure for pattern matching. Compressed suffix arrays are a general class of data structure that improve on the suffix array. These data structures enable quick search for an arbitrary string with a comparatively small index. Given a text ''T'' of ''n'' characters fr ... [...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] |
Compressed Data Structure
The term compressed data structure arises in the computer science subfields of algorithms, data structures, and theoretical computer science. It refers to a data structure whose operations are roughly as fast as those of a conventional data structure for the problem, but whose size can be substantially smaller. The size of the compressed data structure is typically highly dependent upon the entropy of the data being represented. Important examples of compressed data structures include the compressed suffix array and the FM-index,P. Ferragina and G. Manzini, Opportunistic Data Structures with Applications, ''Proceedings of the 41st IEEE Symposium on Foundations of Computer Science'', November 2000, 390-398. Journal version in Indexing Compressed Text, ''Journal of the ACM'', 52(4), 2005, 552-581. both of which can represent an arbitrary text of characters ''T'' for pattern matching. Given any input pattern ''P'', they support the operation of finding if and where ''P'' appears i ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Pattern Matching
In computer science, pattern matching is the act of checking a given sequence of tokens for the presence of the constituents of some pattern. In contrast to pattern recognition, the match usually has to be exact: "either it will or will not be a match." The patterns generally have the form of either sequences or tree structures. Uses of pattern matching include outputting the locations (if any) of a pattern within a token sequence, to output some component of the matched pattern, and to substitute the matching pattern with some other token sequence (i.e., search and replace). Sequence patterns (e.g., a text string) are often described using regular expressions and matched using techniques such as backtracking. Tree patterns are used in some programming languages as a general tool to process data based on its structure, e.g. C#, F#, Haskell, ML, Python, Ruby, Rust, Scala, Swift and the symbolic mathematics language Mathematica have special syntax for expressing tree patt ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Data Structure
In computer science, a data structure is a data organization, management, and storage format that is usually chosen for efficient access to data. More precisely, a data structure is a collection of data values, the relationships among them, and the functions or operations that can be applied to the data, i.e., it is an algebraic structure about data. Usage Data structures serve as the basis for abstract data types (ADT). The ADT defines the logical form of the data type. The data structure implements the physical form of the data type. Different types of data structures are suited to different kinds of applications, and some are highly specialized to specific tasks. For example, relational databases commonly use B-tree indexes for data retrieval, while compiler implementations usually use hash tables to look up identifiers. Data structures provide a means to manage large amounts of data efficiently for uses such as large databases and internet indexing services. Usually, ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Suffix Array
In computer science, a suffix array is a sorted array of all suffixes of a string. It is a data structure used in, among others, full-text indices, data-compression algorithms, and the field of bibliometrics. Suffix arrays were introduced by as a simple, space efficient alternative to suffix trees. They had independently been discovered by Gaston Gonnet in 1987 under the name ''PAT array'' . gave the first in-place \mathcal(n) time suffix array construction algorithm that is optimal both in time and space, where ''in-place'' means that the algorithm only needs \mathcal(1) additional space beyond the input string and the output suffix array. Enhanced suffix arrays (ESAs) are suffix arrays with additional tables that reproduce the full functionality of suffix trees preserving the same time and memory complexity. The suffix array for a subset of all suffixes of a string is called sparse suffix array. Multiple probabilistic algorithms have been developed to minimize the additiona ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
String (computer Science)
In computer programming, a string is traditionally a sequence of characters, either as a literal constant or as some kind of variable. The latter may allow its elements to be mutated and the length changed, or it may be fixed (after creation). A string is generally considered as a data type and is often implemented as an array data structure of bytes (or words) that stores a sequence of elements, typically characters, using some character encoding. ''String'' may also denote more general arrays or other sequence (or list) data types and structures. Depending on the programming language and precise data type used, a variable declared to be a string may either cause storage in memory to be statically allocated for a predetermined maximum length or employ dynamic allocation to allow it to hold a variable number of elements. When a string appears literally in source code, it is known as a string literal or an anonymous string. In formal languages, which are used in mathematical ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Entropy (information Theory)
In information theory, the entropy of a random variable is the average level of "information", "surprise", or "uncertainty" inherent to the variable's possible outcomes. Given a discrete random variable X, which takes values in the alphabet \mathcal and is distributed according to p: \mathcal\to , 1/math>: \Eta(X) := -\sum_ p(x) \log p(x) = \mathbb \log p(X), where \Sigma denotes the sum over the variable's possible values. The choice of base for \log, the logarithm, varies for different applications. Base 2 gives the unit of bits (or " shannons"), while base ''e'' gives "natural units" nat, and base 10 gives units of "dits", "bans", or " hartleys". An equivalent definition of entropy is the expected value of the self-information of a variable. The concept of information entropy was introduced by Claude Shannon in his 1948 paper "A Mathematical Theory of Communication",PDF archived froherePDF archived frohere and is also referred to as Shannon entropy. Shannon's theory defi ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Wavelet Tree
The Wavelet Tree is a succinct data structure to store strings in compressed space. It generalizes the \mathbf_q and \mathbf_q operations defined on bitvectors to arbitrary alphabets. Originally introduced to represent compressed suffix arrays, it has found application in several contexts. The tree is defined by recursively partitioning the alphabet into pairs of subsets; the leaves correspond to individual symbols of the alphabet, and at each node a bitvector stores whether a symbol of the string belongs to one subset or the other. The name derives from an analogy with the wavelet transform for signals, which recursively decomposes a signal into low-frequency and high-frequency components. Properties Let \Sigma be a finite alphabet with \sigma=, \Sigma, . By using succinct dictionaries in the nodes, a string s \in \Sigma^* can be stored in , s, H_0(s) + o(, s, \log \sigma), where H_0(s) is the order-0 empirical entropy of s. If the tree is balanced, the operations \mathbf ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Auxiliary Memory
Computer data storage is a technology consisting of computer components and recording media that are used to retain digital data. It is a core function and fundamental component of computers. The central processing unit (CPU) of a computer is what manipulates data by performing computations. In practice, almost all computers use a storage hierarchy, which puts fast but expensive and small storage options close to the CPU and slower but less expensive and larger options further away. Generally, the fast volatile technologies (which lose data when off power) are referred to as "memory", while slower persistent technologies are referred to as "storage". Even the first computer designs, Charles Babbage's Analytical Engine and Percy Ludgate's Analytical Machine, clearly distinguished between processing and memory (Babbage stored numbers as rotations of gears, while Ludgate stored numbers as displacements of rods in shuttles). This distinction was extended in the Von Neumann arch ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
External Links
An internal link is a type of hyperlink on a web page to another page or resource, such as an image or document, on the same website or domain. Hyperlinks are considered either "external" or "internal" depending on their target or destination. Generally, a link to a page outside the same domain or website is considered external, whereas one that points at another section of the same web page or to another page of the same website or domain is considered internal. These definitions become clouded, however, when the same organization operates multiple domains functioning as a single web experience, e.g. when a secure commerce website is used for purchasing things displayed on a non-secure website. In these cases, links that are "external" by the above definition can conceivably be classified as "internal" for some purposes. Ultimately, an internal link points to a web page or resource in the same root directory. Similarly, seemingly "internal" links are in fact "external" for ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Sequence Alignment
In bioinformatics, a sequence alignment is a way of arranging the sequences of DNA, RNA, or protein to identify regions of similarity that may be a consequence of functional, structural, or evolutionary relationships between the sequences. Aligned sequences of nucleotide or amino acid residues are typically represented as rows within a matrix. Gaps are inserted between the residues so that identical or similar characters are aligned in successive columns. Sequence alignments are also used for non-biological sequences, such as calculating the distance cost between strings in a natural language or in financial data. Interpretation If two sequences in an alignment share a common ancestor, mismatches can be interpreted as point mutations and gaps as indels (that is, insertion or deletion mutations) introduced in one or both lineages in the time since they diverged from one another. In sequence alignments of proteins, the degree of similarity between amino acids occupying a parti ... [...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] |
