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Maximal Unique Match
A maximal unique match or MUM, for short, is part of a key step in the multiple sequence alignment of genomes in computational biology. Identification of MUMs and other potential anchors, is the first step in larger alignment systems such as MUMmer. Anchors are the areas between two genomes where they are highly similar. To understand what a MUM is we each word in the acronym can be broken down individually. Match implies that the substring occurs in both sequences to be aligned. Unique means that the substring occurs only once in each sequence. Finally, maximal states that the substring is not part of another larger string that fulfills both prior requirements. The idea behind this, is that long sequences that match exactly and occur only once in each genome are almost certainly part of the global alignment. Formal definition "Given two genomes A and B, Maximal Unique Match (MUM) substring is a common substring of A and B of length longer than a specified minimum le ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Multiple Sequence Alignment
Multiple sequence alignment (MSA) may refer to the process or the result of sequence alignment of three or more biological sequences, generally protein, DNA, or RNA. In many cases, the input set of query sequences are assumed to have an evolutionary relationship by which they share a linkage and are descended from a common ancestor. From the resulting MSA, sequence homology can be inferred and phylogenetic analysis can be conducted to assess the sequences' shared evolutionary origins. Visual depictions of the alignment as in the image at right illustrate mutation events such as point mutations (single amino acid or nucleotide changes) that appear as differing characters in a single alignment column, and insertion or deletion mutations (indels or gaps) that appear as hyphens in one or more of the sequences in the alignment. Multiple sequence alignment is often used to assess sequence conservation of protein domains, tertiary and secondary structures, and even individual amino acid ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Genomes
In the fields of molecular biology and genetics, a genome is all the genetic information of an organism. It consists of nucleotide sequences of DNA (or RNA in RNA viruses). The nuclear genome includes protein-coding genes and non-coding genes, other functional regions of the genome such as regulatory sequences (see non-coding DNA), and often a substantial fraction of 'junk' DNA with no evident function. Almost all eukaryotes have mitochondria and a small mitochondrial genome. Algae and plants also contain chloroplasts with a chloroplast genome. The study of the genome is called genomics. The genomes of many organisms have been sequenced and various regions have been annotated. The International Human Genome Project reported the sequence of the genome for ''Homo sapiens'' in 200The Human Genome Project although the initial "finished" sequence was missing 8% of the genome consisting mostly of repetitive sequences. With advancements in technology that could handle sequencing ... [...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] |
MUMmer
Mummers' plays are folk plays performed by troupes of amateur actors, traditionally all male, known as mummers or guisers (also by local names such as ''rhymers'', ''pace-eggers'', ''soulers'', ''tipteerers'', ''wrenboys'', and ''galoshins''). Historically, mummers' plays consisted of informal groups of costumed community members that visited from house to house on various holidays. Today the term refers especially to a play in which a number of characters are called on stage, two of whom engage in a combat, the loser being revived by a doctor character. This play is sometimes found associated with a sword dance though both also exist in Britain independently. Mumming spread from the British Isles to a number of former British colonies. It is sometimes performed in the street but more usually during visits to houses and pubs. It is generally performed seasonally or annually, often at Christmas, Easter or on Plough Monday, more rarely on Halloween or All Souls' Day, and often wit ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
LCP Array
In computer science, the longest common prefix array (LCP array) is an auxiliary data structure to the suffix array. It stores the lengths of the longest common prefixes (LCPs) between all pairs of consecutive suffixes in a sorted suffix array. For example, if ''A'' := aab,_ab,_abaab,_b,_baab.html" ;"title="samp>aab, ab, abaab, b, baab">samp>aab, ab, abaab, b, baabis a suffix array, the longest common prefix between ''A'' = aab and ''A'' = ab is ''a'' which has length 1, so ''H'' = 1 in the LCP array ''H''. Likewise, the LCP of ''A'' = ab and ''A'' = abaab is ab, so ''H'' = 2. Augmenting the suffix array with the LCP array allows one to efficiently simulate top-down and bottom-up traversals of the suffix tree, speeds up pattern matching on the suffix array and is a prerequisite for compressed suffix trees. History The LCP array was introduced in 1993, by Udi Manber and Gene Myers alongside the suffix array in order to improve the running time of their string search algorit ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Generalized 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 str ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Local Alignment
Local may refer to: Geography and transportation * Local (train), a train serving local traffic demand * Local, Missouri, a community in the United States * Local government, a form of public administration, usually the lowest tier of administration * Local news, coverage of events in a local context which would not normally be of interest to those of other localities * Local union, a locally based trade union organization which forms part of a larger union Arts, entertainment, and media * ''Local'' (comics), a limited series comic book by Brian Wood and Ryan Kelly * ''Local'' (novel), a 2001 novel by Jaideep Varma * Local TV LLC, an American television broadcasting company * Locast, a non-profit streaming service offering local, over-the-air television * ''The Local'' (film), a 2008 action-drama film * '' The Local'', English-language news websites in several European countries Computing * .local, a network address component * Local variable, a variable that is given lo ... [...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] |
Multiple Sequence Alignment
Multiple sequence alignment (MSA) may refer to the process or the result of sequence alignment of three or more biological sequences, generally protein, DNA, or RNA. In many cases, the input set of query sequences are assumed to have an evolutionary relationship by which they share a linkage and are descended from a common ancestor. From the resulting MSA, sequence homology can be inferred and phylogenetic analysis can be conducted to assess the sequences' shared evolutionary origins. Visual depictions of the alignment as in the image at right illustrate mutation events such as point mutations (single amino acid or nucleotide changes) that appear as differing characters in a single alignment column, and insertion or deletion mutations (indels or gaps) that appear as hyphens in one or more of the sequences in the alignment. Multiple sequence alignment is often used to assess sequence conservation of protein domains, tertiary and secondary structures, and even individual amino acid ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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