|
Dinucleotide 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] |
Protein Tandem Repeats
An array of protein tandem repeats is defined as several (at least two) adjacent copies having the same or similar sequence motifs. These periodic sequences are generated by internal duplications in both coding and non-coding genomic sequences. Repetitive units of protein tandem repeats are considerably diverse, ranging from the repetition of a single amino acid to domains of 100 or more residues. "Repeats" in proteins In proteins, a "repeat" is any sequence block that returns more than one time in the sequence, either in an identical or a highly similar form. The degree of similarity can be highly variable, with some repeats maintaining only a few conserved amino acid positions and a characteristic length. Highly degenerate repeats can be very difficult to detect from sequence alone. Structural similarity can help to identify repetitive patterns in sequence. Structure Repetitiveness does not in itself indicate anything about the structure of the protein. As a "rule of thu ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Genealogical DNA Test
A genealogical DNA test is a DNA-based test used in genetic genealogy that looks at specific locations of a person's genome in order to find or verify ancestral genealogical relationships, or (with lower reliability) to estimate the ethnic mixture of an individual. Since different testing companies use different ethnic reference groups and different matching algorithms, ethnicity estimates for an individual vary between tests, sometimes dramatically. Three principal types of genealogical DNA tests are available, with each looking at a different part of the genome and being useful for different types of genealogical research: autosomal (atDNA), mitochondrial (mtDNA), and Y-DNA. Autosomal tests may result in a large number of DNA matches to both males and females who have also tested with the same company. Each match will typically show an estimated degree of relatedness, i.e., a close family match, 1st-2nd cousins, 3rd-4th cousins, etc. The furthest degree of relationship is u ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Variable Number Tandem Repeat
A variable number tandem repeat (or VNTR) is a location in a genome where a short nucleotide sequence is organized as a tandem repeat. These can be found on many chromosomes, and often show variations in length (number of repeats) among individuals. Each variant acts as an inherited allele, allowing them to be used for personal or parental identification. Their analysis is useful in genetics and biology research, forensics, and DNA fingerprinting. Structure and allelic variation In the schematic above, the rectangular blocks represent each of the repeated DNA sequences at a particular VNTR location. The repeats are in tandem – i.e. they are clustered together and oriented in the same direction. Individual repeats can be removed from (or added to) the VNTR via recombination or replication errors, leading to alleles with different numbers of repeats. Flanking regions are segments of non-repetitive sequence (shown here as thin lines), allowing the VNTR blocks to be ex ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Tandem Repeat Locus
Variable number of tandem repeat locus (VNTR locus) is any DNA sequence that exist in multiple copies strung together in a variety of tandem lengths. The number of repeat copies present at a locus can be visualized by means of a Multi-locus or Multiple Loci VNTR Analysis (MLVA). In short, oligonucleotide primers are developed for each specific tandem repeat locus, followed by PCR and agarose gel electrophoresis Agarose gel electrophoresis is a method of gel electrophoresis used in biochemistry, molecular biology, genetics, and clinical chemistry to separate a mixed population of macromolecules such as DNA or proteins in a matrix of agarose, one of the .... When the length of the repeat and the size of the flanking regions is known, the number of repeats can be calculated. Analysis of multiple loci will result in a genotype. References Genetics {{Genetics-stub ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Tandem Repeats Database
The Tandem Repeats Database (TRDB) is a database of tandem repeats in genomic DNA. See also * Tandem repeat 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 armadil ...s References External links * https://tandem.bu.edu/cgi-bin/trdb/trdb.exe Genetics databases Repetitive DNA sequences {{Biodatabase-stub ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Satellite DNA
Satellite DNA consists of very large arrays of tandemly repeating, non-coding DNA. Satellite DNA is the main component of functional centromeres, and form the main structural constituent of heterochromatin. The name "satellite DNA" refers to the phenomenon that repetitions of a short DNA sequence tend to produce a different frequency of the bases adenine, cytosine, guanine, and thymine, and thus have a different density from bulk DNA such that they form a second or "satellite" band(s) when genomic DNA is separated along a cesium chloride density gradient using buoyant density centrifugation. Sequences with a greater ratio of A+T display a lower density while those with a greater ratio of G+C display a higher density than the bulk of genomic DNA. Some repetitive sequences are ~50% G+C/A+T and thus have buoyant densities the same as bulk genomic DNA. These satellites are called "cryptic" satellites because they form a band hidden within the main band of genomic DNA. "Isopycnic" is ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
ProRepeat
ProRepeat is a database of protein repeats.{{cite journal , last=Luo, first=Hong, author2=Lin Ke , author3=David Audrey , author4=Nijveen Harm , author5=Leunissen Jack A M , date=Jan 2012, title=ProRepeat: an integrated repository for studying amino acid tandem repeats in proteins, journal = Nucleic Acids Res., volume=40, issue=Database issue, pages=D394-9, location = England, pmid = 22102581, doi = 10.1093/nar/gkr1019, pmc =3245022 See also * Tandem repeat 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 armadil ... References External links * http://prorepeat.bioinformatics.nl/ Biological databases Protein structure ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Minisatellite
A minisatellite is a tract of repetitive DNA in which certain DNA motifs (ranging in length from 10–60 base pairs) are typically repeated 5-50 times. Minisatellites occur at more than 1,000 locations in the human genome and they are notable for their high mutation rate and high diversity in the population. Minisatellites are prominent in the centromeres and telomeres of chromosomes, the latter protecting the chromosomes from damage. The name "satellite" refers to the early observation that centrifugation of genomic DNA in a test tube separates a prominent layer of bulk DNA from accompanying "satellite" layers of repetitive DNA. Minisatellites are small sequences of DNA that do not encode proteins but appear throughout the genome hundreds of times, with many repeated copies lying next to each other. Minisatellites and their shorter cousins, the microsatellites, together are classified as VNTR (variable number of tandem repeats) DNA. Confusingly, minisatellites are often referred ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Microsatellite
A microsatellite is a tract of repetitive DNA in which certain DNA motifs (ranging in length from one to six or more base pairs) are repeated, typically 5–50 times. Microsatellites occur at thousands of locations within an organism's genome. They have a higher mutation rate than other areas of DNA leading to high genetic diversity. Microsatellites are often referred to as short tandem repeats (STRs) by forensic geneticists and in genetic genealogy, or as simple sequence repeats (SSRs) by plant geneticists. Microsatellites and their longer cousins, the minisatellites, together are classified as VNTR (variable number of tandem repeats) DNA. The name "satellite" DNA refers to the early observation that centrifugation of genomic DNA in a test tube separates a prominent layer of bulk DNA from accompanying "satellite" layers of repetitive DNA. They are widely used for DNA profiling in cancer diagnosis, in kinship analysis (especially paternity testing) and in forensic identific ... [...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 additiona ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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] |
