Tandem repeat
Encyclopedia
Tandem repeats occur in DNA
when a pattern of two or more nucleotides is repeated and the repetitions are directly adjacent to each other.
in which the sequence A-T-T-C-G is repeated three times.
. Those with fewer are known as microsatellites or short tandem repeat
s.
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...), and abnormalities in such regions can give rise to trinucleotide repeat disorders
.
When the number is not known, variable, or irrelevant, it is sometimes called a variable number tandem repeat
(VNTR). MeSH
classifies variable number tandem repeats under minisatellites.
Tandem repeats can be very useful in determining parentage. Short tandem repeat
s are used for certain genealogical DNA test
s.
DNA
is examined from microsatellites within the chromosomal DNA.
Minisatellite
is another way of saying special regions of the loci
.
Polymerase chain reaction
(or PCR) is performed on the minisatellite areas.
The PCR must be performed on each organism being tested.
The amplified material is then run through electrophoresis
.
By checking the percentage of bands that match, parentage is determined.
In the field of Computer Science
, tandem repeats in strings (e.g. DNA sequences) can be efficiently detected using suffix trees
or suffix arrays
.
Studies in 2004 linked the unusual genetic plasticity of dog
s to mutations in tandem repeats.
DNA
Deoxyribonucleic acid is a nucleic acid that contains the genetic instructions used in the development and functioning of all known living organisms . The DNA segments that carry this genetic information are called genes, but other DNA sequences have structural purposes, or are involved in...
when a pattern of two or more nucleotides is repeated and the repetitions are directly adjacent to each other.
Example
An example would be:- A-T-T-C-G-A-T-T-C-G-A-T-T-C-G
in which the sequence A-T-T-C-G is repeated three times.
Terminology
When between 10 and 60 nucleotides are repeated, it is called a minisatelliteMinisatellite
A minisatellite is a section of DNA that consists of a short series of bases 10-60 bp. These occur at more than 1,000 locations in the human genome...
. Those with fewer are known as microsatellites or short tandem repeat
Short tandem repeat
A short tandem repeat in DNA occurs when a pattern of two or more nucleotides are repeated and the repeated sequences are directly adjacent to each other. The pattern can range in length from 2 to 5 base pairs and is typically in the non-coding intron region...
s.
When exactly two nucleotides are repeated, it is called a "dinucleotide repeat" (for example: ACACACAC...). The microsatellite instability
Microsatellite instability
Microsatellites are repeated sequences of DNA. Although the length of these microsatellites is highly variable from person to person, each individual has microsatellites of a set length. These repeated sequences are common, and normal...
in hereditary nonpolyposis colon cancer most commonly affects such regions.
When three nucleotides are repeated, it is called a "trinucleotide repeat" (for example: CAGCAGCAGCAG...), and abnormalities in such regions can give rise to trinucleotide repeat disorders
Trinucleotide repeat disorders
Trinucleotide repeat disorders are a set of genetic disorders caused by trinucleotide repeat expansion, a kind of mutation where trinucleotide repeats in certain genes exceeding the normal, stable, threshold, which differs per gene...
.
When the number is not known, variable, or irrelevant, it is sometimes called a variable number tandem repeat
Variable number tandem repeat
A Variable Number Tandem Repeat 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 between individuals. Each variant acts as an inherited allele, allowing them to be used for...
(VNTR). MeSH
Medical Subject Headings
Medical Subject Headings is a comprehensive controlled vocabulary for the purpose of indexing journal articles and books in the life sciences; it can also serve as a thesaurus that facilitates searching...
classifies variable number tandem repeats under minisatellites.
Uses
Tandem repeat describes a pattern that helps determine an individual's inherited traits.Tandem repeats can be very useful in determining parentage. Short tandem repeat
Short tandem repeat
A short tandem repeat in DNA occurs when a pattern of two or more nucleotides are repeated and the repeated sequences are directly adjacent to each other. The pattern can range in length from 2 to 5 base pairs and is typically in the non-coding intron region...
s are used for certain genealogical DNA test
Genealogical DNA test
A genealogical DNA test examines the nucleotides at specific locations on a person's DNA for genetic genealogy purposes. The test results are not meant to have any informative medical value and do not determine specific genetic diseases or disorders ; they are intended only to give genealogical...
s.
DNA
DNA
Deoxyribonucleic acid is a nucleic acid that contains the genetic instructions used in the development and functioning of all known living organisms . The DNA segments that carry this genetic information are called genes, but other DNA sequences have structural purposes, or are involved in...
is examined from microsatellites within the chromosomal DNA.
Minisatellite
Minisatellite
A minisatellite is a section of DNA that consists of a short series of bases 10-60 bp. These occur at more than 1,000 locations in the human genome...
is another way of saying special regions of the loci
Locus (genetics)
In the fields of genetics and genetic computation, a locus is the specific location of a gene or DNA sequence on a chromosome. A variant of the DNA sequence at a given locus is called an allele. The ordered list of loci known for a particular genome is called a genetic map...
.
Polymerase chain reaction
Polymerase chain reaction
The polymerase chain reaction is a scientific technique in molecular biology to amplify a single or a few copies of a piece of DNA across several orders of magnitude, generating thousands to millions of copies of a particular DNA sequence....
(or PCR) is performed on the minisatellite areas.
The PCR must be performed on each organism being tested.
The amplified material is then run through electrophoresis
Electrophoresis
Electrophoresis, also called cataphoresis, is the motion of dispersed particles relative to a fluid under the influence of a spatially uniform electric field. This electrokinetic phenomenon was observed for the first time in 1807 by Reuss , who noticed that the application of a constant electric...
.
By checking the percentage of bands that match, parentage is determined.
In the field of Computer Science
Computer science
Computer science or computing science is the study of the theoretical foundations of information and computation and of practical techniques for their implementation and application in computer systems...
, tandem repeats in strings (e.g. DNA sequences) can be efficiently detected using suffix trees
Suffix tree
In computer science, a suffix tree is a data structure that presents the suffixes of a given string in a way that allows for a particularly fast implementation of many important string operations.The suffix tree for a string S is a tree whose edges are labeled with strings, such that each suffix...
or suffix arrays
Suffix array
In computer science, a suffix array is an array of integers giving the starting positions of suffixes of a string in lexicographical order.-Details:Consider the string...
.
Studies in 2004 linked the unusual genetic plasticity of dog
Dog
The domestic dog is a domesticated form of the gray wolf, a member of the Canidae family of the order Carnivora. The term is used for both feral and pet varieties. The dog may have been the first animal to be domesticated, and has been the most widely kept working, hunting, and companion animal in...
s to mutations in tandem repeats.
See also
- Variable number tandem repeatVariable number tandem repeatA Variable Number Tandem Repeat 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 between individuals. Each variant acts as an inherited allele, allowing them to be used for...
s - Short tandem repeatShort tandem repeatA short tandem repeat in DNA occurs when a pattern of two or more nucleotides are repeated and the repeated sequences are directly adjacent to each other. The pattern can range in length from 2 to 5 base pairs and is typically in the non-coding intron region...
s - Satellite DNASatellite DNASatellite 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....
- MinisatelliteMinisatelliteA minisatellite is a section of DNA that consists of a short series of bases 10-60 bp. These occur at more than 1,000 locations in the human genome...
- Microsatellite
- Tandem repeats databaseTandem repeats databaseThe Tandem Repeats Database is a database of tandem repeats in genomic DNA....
- Amino acid tandem repeat
External links
- Examples :
- VNTRs - info and animated example
- Databases :
- Search tools :
- Tandem Repeats Finder
- Mreps
- STAR
- TRED - Tandem Repeats over the Edit Distance
- TandemSWAN
- Microsatellite repeats finder
- JSTRING - Java Search for Tandem Repeats in genomes
- Phobos - a tandem repeat search tool for perfect and imperfect repeats - the maximum pattern size depends only on computational power
- UGENE - an ultra fast and memory efficient open-source tandem repeats finder implementation.