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Suffix Tree
In computer science, a suffix tree (also called PAT tree or, in an earlier form, position tree) is a compressed trie containing all the suffixes of the given text as their keys and positions in the text as their values. Suffix trees allow particularly fast implementations of many important string operations. The construction of such a tree for the string S takes time and space linear in the length of S. Once constructed, several operations can be performed quickly, for instance locating a substring in S, locating a substring if a certain number of mistakes are allowed, locating matches for a regular expression pattern etc. Suffix trees also provide one of the first linear-time solutions for the longest common substring problem. These speedups come at a cost: storing a string's suffix tree typically requires significantly more space than storing the string itself. History The concept was first introduced by . Rather than the suffix S ..n/math>, Weiner stored in his trie the ''pref ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Suffix Tree BANANA
In linguistics, a suffix is an affix which is placed after the stem of a word. Common examples are case endings, which indicate the grammatical case of nouns, adjectives, and verb endings, which form the conjugation of verbs. Suffixes can carry grammatical information (inflectional suffixes) or lexical information ( derivational/lexical suffixes'').'' An inflectional suffix or a grammatical suffix. Such inflection changes the grammatical properties of a word within its syntactic category. For derivational suffixes, they can be divided into two categories: class-changing derivation and class-maintaining derivation. Particularly in the study of Semitic languages, suffixes are called affirmatives, as they can alter the form of the words. In Indo-European studies, a distinction is made between suffixes and endings (see Proto-Indo-European root). Suffixes can carry grammatical information or lexical information. A word-final segment that is somewhere between a free morpheme and a boun ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Generalised Suffix Tree
In computer science, a generalized suffix tree is a suffix tree for a set of strings. Given the set of strings D=S_1,S_2,\dots,S_d of total length n, it is a Patricia tree containing all n suffixes of the strings. It is mostly used in bioinformatics. Functionality It can be built in \Theta(n) time and space, and can be used to find all z occurrences of a string P of length m in O(m + z) time, which is asymptotically optimal (assuming the size of the alphabet is constant). When constructing such a tree, each string should be padded with a unique out-of-alphabet marker symbol (or string) to ensure no suffix is a substring of another, guaranteeing each suffix is represented by a unique leaf node. Algorithms for constructing a GST include Ukkonen's algorithm (1995) and McCreight's algorithm (1976). Example A suffix tree for the strings ABAB and BABA is shown in a figure above. They are padded with the unique terminator strings $0 and $1. The numbers in the leaf nodes are string ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Data Compression
In information theory, data compression, source coding, or bit-rate reduction is the process of encoding information using fewer bits than the original representation. Any particular compression is either lossy or lossless. Lossless compression reduces bits by identifying and eliminating statistical redundancy. No information is lost in lossless compression. Lossy compression reduces bits by removing unnecessary or less important information. Typically, a device that performs data compression is referred to as an encoder, and one that performs the reversal of the process (decompression) as a decoder. The process of reducing the size of a data file is often referred to as data compression. In the context of data transmission, it is called source coding; encoding done at the source of the data before it is stored or transmitted. Source coding should not be confused with channel coding, for error detection and correction or line coding, the means for mapping data onto a signal. ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Protein
Proteins are large biomolecules and macromolecules that comprise one or more long chains of amino acid residues. Proteins perform a vast array of functions within organisms, including catalysing metabolic reactions, DNA replication, responding to stimuli, providing structure to cells and organisms, and transporting molecules from one location to another. Proteins differ from one another primarily in their sequence of amino acids, which is dictated by the nucleotide sequence of their genes, and which usually results in protein folding into a specific 3D structure that determines its activity. A linear chain of amino acid residues is called a polypeptide. A protein contains at least one long polypeptide. Short polypeptides, containing less than 20–30 residues, are rarely considered to be proteins and are commonly called peptides. The individual amino acid residues are bonded together by peptide bonds and adjacent amino acid residues. The sequence of amino acid residue ... [...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] |
String Search
In computer science, string-searching algorithms, sometimes called string-matching algorithms, are an important class of string algorithms that try to find a place where one or several strings (also called patterns) are found within a larger string or text. A basic example of string searching is when the pattern and the searched text are arrays of elements of an alphabet (finite set) Σ. Σ may be a human language alphabet, for example, the letters ''A'' through ''Z'' and other applications may use a ''binary alphabet'' (Σ = ) or a ''DNA alphabet'' (Σ = ) in bioinformatics. In practice, the method of feasible string-search algorithm may be affected by the string encoding. In particular, if a variable-width encoding is in use, then it may be slower to find the ''N''th character, perhaps requiring time proportional to ''N''. This may significantly slow some search algorithms. One of many possible solutions is to search for the sequence of code units instead, but doing so may produ ... [...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] |
Longest Palindromic Substring
In computer science, the longest palindromic substring or longest symmetric factor problem is the problem of finding a maximum-length contiguous substring of a given string that is also a palindrome. For example, the longest palindromic substring of "bananas" is "anana". The longest palindromic substring is not guaranteed to be unique; for example, in the string "abracadabra", there is no palindromic substring with length greater than three, but there are two palindromic substrings with length three, namely, "aca" and "ada". In some applications it may be necessary to return all maximal palindromic substrings (that is, all substrings that are themselves palindromes and cannot be extended to larger palindromic substrings) rather than returning only one substring or returning the maximum length of a palindromic substring. invented an O(n)-time algorithm for listing all the palindromes that appear at the start of a given string of length n. However, as observed e.g., by , the same algo ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Tandem Repeats
Tandem repeats occur in DNA when a pattern of one or more nucleotides is repeated and the repetitions are directly adjacent to each other. Several protein domains also form tandem repeats within their amino acid primary structure, such as armadillo repeats. However, in proteins, perfect tandem repeats are unlikely in most ''in vivo'' proteins, and most known repeats are in proteins which have been designed. An example would be: : ATTCG ATTCG ATTCG in which the sequence ATTCG is repeated three times. Terminology When between 10 and 60 nucleotides are repeated, it is called a minisatellite. Those with fewer are known as microsatellites or short tandem repeats. When exactly two nucleotides are repeated, it is called a ''dinucleotide repeat'' (for example: ACACACAC...). The microsatellite instability in hereditary nonpolyposis colon cancer most commonly affects such regions. When three nucleotides are repeated, it is called a ''trinucleotide repeat'' (for example: CAGCAGCAGCAG...), ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Palindrome
A palindrome is a word, number, phrase, or other sequence of symbols that reads the same backwards as forwards, such as the words ''madam'' or ''racecar'', the date and time ''11/11/11 11:11,'' and the sentence: "A man, a plan, a canal – Panama". The 19-letter Finnish word ''saippuakivikauppias'' (a soapstone vendor), is the longest single-word palindrome in everyday use, while the 12-letter term ''tattarrattat'' (from James Joyce in ''Ulysses'') is the longest in English. The word ''palindrome'' was introduced by English poet and writer Henry Peacham in 1638.Henry Peacham, ''The Truth of our Times Revealed out of One Mans Experience'', 1638p. 123/ref> The concept of a palindrome can be dated to the 3rd-century BCE, although no examples survive; the first physical examples can be dated to the 1st-century CE with the Latin acrostic word square, the Sator Square (contains both word and sentence palindromes), and the 4th-century Greek Byzantine sentence palindrome ''nipson ano ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Lowest Common Ancestor
In graph theory and computer science, the lowest common ancestor (LCA) (also called least common ancestor) of two nodes and in a Tree (graph theory), tree or directed acyclic graph (DAG) is the lowest (i.e. deepest) node that has both and as descendants, where we define each node to be a descendant of itself (so if has a direct connection from , is the lowest common ancestor). The LCA of and in is the shared ancestor of and that is located farthest from the root. Computation of lowest common ancestors may be useful, for instance, as part of a procedure for determining the distance between pairs of nodes in a tree: the distance from to can be computed as the distance from the root to , plus the distance from the root to , minus twice the distance from the root to their lowest common ancestor . In ontology (information science), ontologies, the lowest common ancestor is also known as the least common ancestor. In a tree data structure where each node points to its pa ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Longest Repeated Substring Problem
In computer science, the longest repeated substring problem is the problem of finding the longest substring of a string that occurs at least twice. This problem can be solved in linear time and space \Theta(n) by building a suffix tree In computer science, a suffix tree (also called PAT tree or, in an earlier form, position tree) is a compressed trie containing all the suffixes of the given text as their keys and positions in the text as their values. Suffix trees allow particu ... for the string (with a special end-of-string symbol like '$' appended), and finding the deepest internal node in the tree with more than one child. Depth is measured by the number of characters traversed from the root. The string spelled by the edges from the root to such a node is a longest repeated substring. The problem of finding the longest substring with at least k occurrences can be solved by first preprocessing the tree to count the number of leaf descendants for each internal node, and then ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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