Tandem repeat
In
An example would be:
- ATTCG ATTCG ATTCG
in which the sequence ATTCG is repeated three times.
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 them to be separated from the rest of the genome with density-based laboratory techniques, thus appearing as "satellite bands." Albeit, a tandem repeat array could not show up as a satellite band if it had a nucleotide composition close to the average of the genome.[citation needed]
When exactly two nucleotides are repeated, it is called a dinucleotide repeat (for example: ACACACAC...). The
When three nucleotides are repeated, it is called a trinucleotide repeat (for example: CAGCAGCAGCAG...), and abnormalities in such regions can give rise to
When between 10 and 60 nucleotides are repeated, it is called a
When much larger lengths of nucleotides are repeated, on the order of 1,000 nucleotides, it is called a macrosatellite.
When the repeat unit copy number is variable in the population being considered, it is called a variable number tandem repeat (VNTR). MeSH classifies variable number tandem repeats under minisatellites.[4]
Mechanism
Tandem repeats can occur through different mechanisms. For example, slipped strand mispairing (SSM), (also known as
Other mechanisms include
Uses
Tandem repeat describes a pattern that helps determine an individual's inherited traits.
Tandem repeats can be very useful in determining
Polymorphic tandem repeats (alias VNTRs) are also present in microorganisms and can be used to trace the origin of an outbreak. The corresponding assay in which a collection of VNTRs is typed to characterize a strain is most often called
In the field of
Studies in 2004 linked the unusual genetic plasticity of dogs to mutations in tandem repeats.[6]
Nested tandem repeats are described as repeating unit lengths that are variable or unknown and frequently include an asymmetric hierarchy of smaller repeating units. These repeats are constructed from distinct groups of homologous-length monomers. An algorithm known as NTRprism was created by Oxford Nanopore Technologies researchers to enable for the annotation of repetitive structures in built satellite DNA arrays. The algorithm NTRprism is developed to find and display the satellite repeating periodicity.[7]
See also
- Microsatellite
- Minisatellite
- ProRepeat
- Satellite DNA
- Tandem Repeats Database
- Tandem repeat locus
- Variable number tandem repeats
References
- ^ Tandem+Repeat at the U.S. National Library of Medicine Medical Subject Headings (MeSH)
- PMID 20553501.
- PMID 10321739.
- ^ Variable+Number+of+Tandem+Repeats at the U.S. National Library of Medicine Medical Subject Headings (MeSH)
- PMID 36495863.
- S2CID 10680162.
- PMID 35357911.
External links
- Examples:
- VNTRs - info and animated example
- Databases:
- Search tools:
- TAPO: A combined method for the identification of tandem repeats in protein structures
- Tandem Repeats Finder
- Mreps
- STAR
- Splinter
- 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.
- TRAL: Tandem Repeat Annotation Library - a meta-predictor tool with statistical filtering, with a range of functions for repeat annotation and analyses