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FM-index
In computer science, an FM-index is a compressed full-text substring index based on the Burrows–Wheeler transform, with some similarities to the suffix array. It was created by Paolo Ferragina and Giovanni Manzini,Paolo Ferragina and Giovanni Manzini (2000)"Opportunistic Data Structures with Applications".Proceedings of the 41st Annual Symposium on Foundations of Computer Science. p.390. who describe it as an opportunistic data structure as it allows compression of the input text while still permitting fast substring queries. The name stands for Full-text index in Minute space. It can be used to efficiently find the number of occurrences of a pattern within the compressed text, as well as locate the position of each occurrence. The query time, as well as the required storage space, has a sublinear complexity with respect to the size of the input data. The original authors have devised improvements to their original approach and dubbed it "FM-Index version 2". A further improvem ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Burrows–Wheeler Transform
The Burrows–Wheeler transform (BWT, also called block-sorting compression) rearranges a character string into runs of similar characters. This is useful for compression, since it tends to be easy to compress a string that has runs of repeated characters by techniques such as move-to-front transform and run-length encoding. More importantly, the transformation is ''reversible'', without needing to store any additional data except the position of the first original character. The BWT is thus a "free" method of improving the efficiency of text compression algorithms, costing only some extra computation. The Burrows–Wheeler transform is an algorithm used to prepare data for use with data compression techniques such as bzip2. It was invented by Michael Burrows and David Wheeler in 1994 while Burrows was working at DEC Systems Research Center in Palo Alto, California. It is based on a previously unpublished transformation discovered by Wheeler in 1983. The algorithm can be imp ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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] |
Substring Index
In computer science, a substring index is a data structure which gives substring search in a text or text collection in sublinear time. If you have a document S of length n, or a set of documents D=\ of total length n, you can locate all occurrences of a pattern P in o(n) time. (See Big O notation.) The phrase full-text index is also often used for an index of all substrings of a text. But is ambiguous, as it is also used for regular word indexes such as inverted files and document retrieval. See full text search. Substring indexes include: * Suffix tree * Suffix array * N-gram index, an inverted file for all N-grams of the text * Compressed suffix arrayR. Grossi and J. S. VitterCompressed Suffix Arrays and Suffix Trees, with Applications to Text Indexing and String Matching ''SIAM Journal on Computing,'' 35(2), 2005, 378-407. * FM-index In computer science, an FM-index is a compressed full-text substring index based on the Burrows–Wheeler transform, with some similarities to t ... [...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 addit ... [...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 \math ... [...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 addit ... [...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 pa ... [...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 practical disciplines (including the design and implementation of hardware and software). Computer science is generally considered an area of 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 problems that can be solved using them. The fields of cryptography and computer security involve studying the means for secure communication and for preventing security vulnerabilities. Computer graphics and computational geometry address the generation of images. Programming language theory considers different ways to describe computational processes, and database theory concerns the management of repositories ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
DSPACE
DSpace is an open source repository software package typically used for creating open access repositories for scholarly and/or published digital content. While DSpace shares some feature overlap with content management systems and document management systems, the DSpace repository software serves a specific need as a digital archives system, focused on the long-term storage, access and preservation of digital content. The optional DSpace registry lists almost three thousand repositories all over the world. History The first public version of DSpace was released in November 2002, as a joint effort between developers from MIT and HP Labs. Following the first user group meeting in March 2004, a group of interested institutions formed the DSpace Federation, which determined the governance of future software development by adopting the Apache Foundation's community development model as well as establishing the DSpace Committer Group. In July 2007 as the DSpace user community grew lar ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Time Complexity
In computer science, the time complexity is the computational complexity that describes the amount of computer time it takes to run an algorithm. Time complexity is commonly estimated by counting the number of elementary operations performed by the algorithm, supposing that each elementary operation takes a fixed amount of time to perform. Thus, the amount of time taken and the number of elementary operations performed by the algorithm are taken to be related by a constant factor. Since an algorithm's running time may vary among different inputs of the same size, one commonly considers the worst-case time complexity, which is the maximum amount of time required for inputs of a given size. Less common, and usually specified explicitly, is the average-case complexity, which is the average of the time taken on inputs of a given size (this makes sense because there are only a finite number of possible inputs of a given size). In both cases, the time complexity is generally express ... [...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 propertie ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Move To Front
The move-to-front (MTF) transform is an encoding of data (typically a stream of bytes) designed to improve the performance of entropy encoding techniques of compression. When efficiently implemented, it is fast enough that its benefits usually justify including it as an extra step in data compression algorithm. This algorithm was first published by B. Ryabko under the name of "book stack" in 1980. Subsequently, it was rediscovered by J.K. Bentley et al. in 1986, as attested in the explanatory note. The transform The main idea is that each symbol in the data is replaced by its index in the stack of “recently used symbols”. For example, long sequences of identical symbols are replaced by as many zeroes, whereas when a symbol that has not been used in a long time appears, it is replaced with a large number. Thus at the end the data is transformed into a sequence of integers; if the data exhibits a lot of local correlations, then these integers tend to be small. Let us give a ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
