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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, such as locating a substring in S, locating a substring if a certain number of mistakes are allowed, and locating matches for a regular expression pattern. Suffix trees also provided 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 ''prefix ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Suffix Tree BANANA
In linguistics, a suffix is an affix which is placed after the Stem (linguistics), stem of a word. Common examples are case endings, which indicate the grammatical case of nouns and adjectives, and verb endings, which form the Grammatical conjugation, conjugation of verbs. Suffixes can carry grammatical information (inflectional endings) or lexical information (derivation (linguistics), derivational/lexical suffixes)''.'' Inflection changes the grammatical properties of a word within its syntactic category. Derivational suffixes fall 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). A word-final segment that is somewhere between a free morpheme and a bound morpheme is known as a suffixoidKremer, Marion. 1997. ''Person ref ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Sorting Algorithm
In computer science, a sorting algorithm is an algorithm that puts elements of a List (computing), list into an Total order, order. The most frequently used orders are numerical order and lexicographical order, and either ascending or descending. Efficient sorting is important for optimizing the Algorithmic efficiency, efficiency of other algorithms (such as search algorithm, search and merge algorithm, merge algorithms) that require input data to be in sorted lists. Sorting is also often useful for Canonicalization, canonicalizing data and for producing human-readable output. Formally, the output of any sorting algorithm must satisfy two conditions: # The output is in monotonic order (each element is no smaller/larger than the previous element, according to the required order). # The output is a permutation (a reordering, yet retaining all of the original elements) of the input. Although some algorithms are designed for sequential access, the highest-performing algorithms assum ... [...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 residue (biochemistry), residues. Proteins perform a vast array of functions within organisms, including Enzyme catalysis, catalysing metabolic reactions, DNA replication, Cell signaling, responding to stimuli, providing Cytoskeleton, structure to cells and Fibrous protein, organisms, and Intracellular transport, transporting molecules from one location to another. Proteins differ from one another primarily in their sequence of amino acids, which is dictated by the Nucleic acid sequence, nucleotide sequence of their genes, and which usually results in protein folding into a specific Protein structure, 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 pep ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Bioinformatics
Bioinformatics () is an interdisciplinary field of science that develops methods and Bioinformatics software, software tools for understanding biological data, especially when the data sets are large and complex. Bioinformatics uses biology, chemistry, physics, computer science, data science, computer programming, information engineering, mathematics and statistics to analyze and interpret biological data. The process of analyzing and interpreting data can sometimes be referred to as computational biology, however this distinction between the two terms is often disputed. To some, the term ''computational biology'' refers to building and using models of biological systems. Computational, statistical, and computer programming techniques have been used for In silico, computer simulation analyses of biological queries. They include reused specific analysis "pipelines", particularly in the field of genomics, such as by the identification of genes and single nucleotide polymorphis ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
String Search
A string-searching algorithm, sometimes called string-matching algorithm, is an algorithm that searches a body of text for portions that match by pattern. 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 produce false matches unless the encoding is specifically designed to avoid it. Overview The most basic c ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Computational Biology
Computational biology refers to the use of techniques in computer science, data analysis, mathematical modeling and Computer simulation, computational simulations to understand biological systems and relationships. An intersection of computer science, biology, and data science, the field also has foundations in applied mathematics, molecular biology, cell biology, chemistry, and genetics. 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 Punched card, punch cards. The amount of data grew exponentially by the end of the 1980s, requiring new computational methods for quickly interpreting relevant information. Per ... [...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 alg ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Tandem Repeats
In genetics, tandem repeats occur in DNA when a pattern of one or more nucleotides is repeated and the repetitions are directly adjacent to each other, e.g. ATTCG ATTCG ATTCG, in which the sequence ATTCG is repeated three times. Several protein domains also form tandem repeats within their amino acid primary structure, such as armadillo repeats. However, in proteins, perfect tandem repeats are rare in naturally proteins, but they have been added to designed proteins. Tandem repeats constitute about 8% of the human genome. They are implicated in more than 50 lethal human diseases, including amyotrophic lateral sclerosis, Huntington's disease, and several cancers. Terminology All tandem repeat arrays are classifiable as satellite DNA, a name originating from the fact that tandem DNA repeats, by nature of repeating the same nucleotide sequences repeatedly, have a unique ratio of the two possible nucleotide base pair combinations, conferring them a specific mass density that allows ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Palindrome
A palindrome (Help:IPA/English, /ˈpæl.ɪn.droʊm/) is a word, palindromic number, number, phrase, or other sequence of symbols that reads the same backwards as forwards, such as ''madam'' or ''racecar'', the date "Twosday, 02/02/2020" and the sentence: "A man, a plan, a canal – Panama". The 19-letter Finnish language, 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 (novel), Ulysses'') is the longest in English. The word ''palindrome'' was introduced by English poet and writer Henry Peacham (born 1578), Henry Peacham in 1638.Henry Peacham, ''The Truth of our Times Revealed out of One Mans Experience'', 1638p. 123 The concept of a palindrome can be dated to the 3rd-century BCE, although no examples survive. The earliest known examples are the 1st-century CE Latin acrostic word square, the Sator Square (which contains both word and senten ... [...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 a tree data structure where each node points to its parent, the lowest common ancestor can be easily determined by finding the first intersection of the paths from and to ... [...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 the ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Lempel–Ziv
LZ77 and LZ78 are the two lossless data compression algorithms published in papers by Abraham Lempel and Jacob Ziv in 1977 and 1978. They are also known as Lempel-Ziv 1 (LZ1) and Lempel-Ziv 2 (LZ2) respectively. These two algorithms form the basis for many variations including LZW, LZSS, LZMA and others. Besides their academic influence, these algorithms formed the basis of several ubiquitous compression schemes, including GIF and the DEFLATE algorithm used in PNG and ZIP. They are both theoretically dictionary coders. LZ77 maintains a sliding window during compression. This was later shown to be equivalent to the ''explicit dictionary'' constructed by LZ78—however, they are only equivalent when the entire data is intended to be decompressed. Since LZ77 encodes and decodes from a sliding window over previously seen characters, decompression must always start at the beginning of the input. Conceptually, LZ78 decompression could allow random access to the input if the en ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
