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Burrows–Wheeler Transform
The Burrows–Wheeler transform (BWT) rearranges a character string into runs of similar characters, in a manner that can be reversed to recover the original string. Since compression techniques such as move-to-front transform and run-length encoding are more effective when such runs are present, the BWT can be used as a preparatory step to improve the efficiency of a compression algorithm, and is used this way in software such as bzip2. The algorithm can be implemented efficiently using a suffix array thus reaching linear time complexity. It was invented by David Wheeler in 1983, and later published by him and Michael Burrows in 1994. Their paper included a compression algorithm, called the Block-sorting Lossless Data Compression Algorithm or BSLDCA, that compresses data by using the BWT followed by move-to-front coding and Huffman coding or arithmetic coding. Description The transform is done by constructing a matrix (known as the Burrows-Wheeler Matrix) whose rows are the ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Character 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 often implemented as an array data structure of bytes (or words) that stores a sequence of elements, typically characters, using some character encoding. More general, ''string'' may also denote a sequence (or list) of data other than just characters. 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 logic and theoretical computer science, a stri ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Lyndon Word
In mathematics, in the areas of combinatorics and computer science, a Lyndon word is a nonempty string that is strictly smaller in lexicographic order than all of its rotations. Lyndon words are named after mathematician Roger Lyndon, who investigated them in 1954, calling them standard lexicographic sequences. Anatoly Shirshov introduced Lyndon words in 1953 calling them regular words. Lyndon words are a special case of Hall words; almost all properties of Lyndon words are shared by Hall words. Definitions Several equivalent definitions exist. A k-ary Lyndon word of length n > 0 is an n-character string over an alphabet of size k, and which is the unique minimum element in the lexicographical ordering in the multiset of all its rotations. Being the singularly smallest rotation implies that a Lyndon word differs from any of its non-trivial rotations, and is therefore aperiodic.; . Alternately, a word w is a Lyndon word if and only if it is nonempty and lexicographically stri ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
ChIP-Seq
ChIP-sequencing, also known as ChIP-seq, is a method used to analyze protein interactions with DNA. ChIP-seq combines chromatin immunoprecipitation (ChIP) with Massively parallel signature sequencing, massively parallel DNA sequencing to identify the binding sites of DNA-associated proteins. It can be used to map global binding sites precisely for any protein of interest. Previously, ChIP-on-chip was the most common technique utilized to study these protein–DNA relations. Uses ChIP-seq is primarily used to determine how transcription factors and other chromatin-associated proteins influence phenotype-affecting mechanisms. Determining how proteins interact with DNA to regulate gene expression is essential for fully understanding many biological processes and disease states. This epigenetic information is complementary to genotype and expression analysis. ChIP-seq technology is currently seen primarily as an alternative to ChIP-chip which requires a protein microarray, hybridization ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Base Pair
A base pair (bp) is a fundamental unit of double-stranded nucleic acids consisting of two nucleobases bound to each other by hydrogen bonds. They form the building blocks of the DNA double helix and contribute to the folded structure of both DNA and RNA. Dictated by specific hydrogen bonding patterns, "Watson–Crick" (or "Watson–Crick–Franklin") base pairs (guanine–cytosine and adenine–thymine) allow the DNA helix to maintain a regular helical structure that is subtly dependent on its nucleotide sequence. The Complementarity (molecular biology), complementary nature of this based-paired structure provides a Redundancy (information theory), redundant copy of the genetic information encoded within each strand of DNA. The regular structure and data redundancy provided by the DNA double helix make DNA well suited to the storage of genetic information, while base-pairing between DNA and incoming nucleotides provides the mechanism through which DNA polymerase replicates DNA and ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
DNA Sequencing
DNA sequencing is the process of determining the nucleic acid sequence – the order of nucleotides in DNA. It includes any method or technology that is used to determine the order of the four bases: adenine, thymine, cytosine, and guanine. The advent of rapid DNA sequencing methods has greatly accelerated biological and medical research and discovery. Knowledge of DNA sequences has become indispensable for basic biological research, Genographic Project, DNA Genographic Projects and in numerous applied fields such as medical diagnosis, biotechnology, forensic biology, virology and biological systematics. Comparing healthy and mutated DNA sequences can diagnose different diseases including various cancers, characterize antibody repertoire, and can be used to guide patient treatment. Having a quick way to sequence DNA allows for faster and more individualized medical care to be administered, and for more organisms to be identified and cataloged. The rapid advancements in DNA seque ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Next-generation Sequencing
Massive parallel sequencing or massively parallel sequencing is any of several high-throughput approaches to DNA sequencing using the concept of massively parallel processing; it is also called next-generation sequencing (NGS) or second-generation sequencing. Some of these technologies emerged between 1993 and 1998 and have been commercially available since 2005. These technologies use miniaturized and parallelized platforms for sequencing of 1 million to 43 billion short reads (50 to 400 bases each) per instrument run. Many NGS platforms differ in engineering configurations and sequencing chemistry. They share the technical paradigm of massive parallel sequencing via spatially separated, clonally amplified DNA templates or single DNA molecules in a flow cell. This design is very different from that of Sanger sequencing—also known as capillary sequencing or first-generation sequencing—which is based on electrophoretic separation of chain-termination products produced in indiv ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Image Compression
Image compression is a type of data compression applied to digital images, to reduce their cost for computer data storage, storage or data transmission, transmission. Algorithms may take advantage of visual perception and the statistical properties of image data to provide superior results compared with generic data compression methods which are used for other digital data. Lossy and lossless image compression Image compression may be lossy compression, lossy or lossless compression, lossless. Lossless compression is preferred for archival purposes and often for medical imaging, technical drawings, clip art, or comics. Lossy compression methods, especially when used at low bit rates, introduce compression artifacts. Lossy methods are especially suitable for natural images such as photographs in applications where minor (sometimes imperceptible) loss of fidelity is acceptable to achieve a substantial reduction in bit rate. Lossy compression that produces negligible differences ... [...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 biology, structural, or evolutionary relationships between the sequences. Aligned sequences of nucleotide or amino acid residues are typically represented as rows within a matrix (mathematics), matrix. Gaps are inserted between the Residue (chemistry), 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 Edit distance, distance cost between strings in a natural language, or to display 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 ali ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Lossless Compression
Lossless compression is a class of data compression that allows the original data to be perfectly reconstructed from the compressed data with no loss of information. Lossless compression is possible because most real-world data exhibits statistical redundancy. By contrast, lossy compression permits reconstruction only of an approximation of the original data, though usually with greatly improved compression rates (and therefore reduced media sizes). By operation of the pigeonhole principle, no lossless compression algorithm can shrink the size of all possible data: Some data will get longer by at least one symbol or bit. Compression algorithms are usually effective for human- and machine-readable documents and cannot shrink the size of random data that contain no redundancy. Different algorithms exist that are designed either with a specific type of input data in mind or with specific assumptions about what kinds of redundancy the uncompressed data are likely to contain. Lo ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Colexicographic Order
In mathematics, the lexicographic or lexicographical order (also known as lexical order, or dictionary order) is a generalization of the alphabetical order of the dictionaries to sequences of ordered symbols or, more generally, of elements of a totally ordered set. There are several variants and generalizations of the lexicographical ordering. One variant applies to sequences of different lengths by comparing the lengths of the sequences before considering their elements. Another variant, widely used in combinatorics, orders subsets of a given finite set by assigning a total order to the finite set, and converting subsets into increasing sequences, to which the lexicographical order is applied. A generalization defines an order on an ''n''-ary Cartesian product of partially ordered sets; this order is a total order if and only if all factors of the Cartesian product are totally ordered. Definition The words in a lexicon (the set of words used in some language) have a conven ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Null Character
The null character is a control character with the value zero. Many character sets include a code point for a null character including Unicode (Universal Coded Character Set), ASCII (ISO/IEC 646), Baudot, ITA2 codes, the C0 control code, and EBCDIC. In modern character sets, the null character has a code point value of zero which is generally translated to a single code unit with a zero value. For instance, in UTF-8, it is a single, zero byte. However, in Modified UTF-8 the null character is encoded as two bytes : . This allows the byte with the value of zero, which is not used for any character, to be used as a string terminator. Originally, its meaning was like NOP when sent to a printer or a terminal, it had no effect (although some terminals incorrectly displayed it as space). When electromechanical teleprinters were used as computer output devices, one or more null characters were sent at the end of each printed line to allow time for the mechanism to return to the fir ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
C0 And C1 Control Codes
The C0 and C1 control code or control character sets define control codes for use in text by computer systems that use ASCII and derivatives of ASCII. The codes represent additional information about the text, such as the position of a cursor, an instruction to start a new line, or a message that the text has been received. C0 codes are the range 00 HEX–1FHEX and the default C0 set was originally defined in ISO 646 (ASCII). C1 codes are the range 80HEX–9FHEX and the default C1 set was originally defined in ECMA-48 (harmonized later with ISO 6429). The ISO/IEC 2022 system of specifying control and graphic characters allows other C0 and C1 sets to be available for specialized applications, but they are rarely used. C0 controls ASCII defines 32 control characters, plus the DEL character. This large number of codes was desirable at the time, as multi-byte controls would require implementation of a state machine in the terminal, which was very difficult with contemporary electr ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
