Microsatellites/Tandem Repeats database
Tandem Repeats are copies of DNA sequences which lie adjacent to each other. When those repeats are short, we will use the term Microsatellite Repeats: a variety of simple di-, tri-, tetra-, and pentanucleotide tandem repeats (usually less than 100 bases long). Other names we may used to describe this repetitive sequences areVariable Number Tandem Repeats, Short Sequence Repeats (SSRs), Exact Tandem Repeats (ETRs), Repetitive DNA, SSR (Simple Sequence Repeats), Simple Tandem Repeats (STR)
We have developed a Microsatellite
Repeats finder, and it has been used for detection of
microsatellites in all up to date sequenced prokaryotic chromosomes.
The data obtained is searchable throw this site.
To search presence of microsatellite repeats in one specific
genome, select the genera in main page and the
genome in the corresponding form. Percentage
of mismatches in the form may be 0, 0.1, 0.2
or 0.3, which represents percentage
of mismatches allowed within the tandem repeats. When this
number is 0, we will get perfect tandem repeats (Exatc Tandem Repeats
or ETRs). The number of microsatellite repeats is very small in
prokaryotes when comparing to eukaryotes. In fact, no Exact Tandem
Repeats were detected in several prokaryotic genomes. A link in results
page will allow easily designing
primers (with primer3) for amplification of a DNA
fragments which includes the microsatellite repeat.
Although this data may be used for research, our
basic purpose is educational: users will be able to simulate
microsatellite based genotyping, so that they will be able to easily
understand the technique. We encourage
user
to design primers and to perform PCR amplifications (also
available in this site) to check whether it could be used to discern
between genomes within the species. Often, the PCR simulation
tool will not yield amplicons when checking a genome different to that
one used for primer design. In fact, the usage of tandem repeats for
epidemiology purposes in bacteria has been limited to a few species.
A more complete microsatellites database is available
at Multiple Locus
VNTR Analysis
(MLVA) website. Users will easily find differences between results at MLVA
and our database. The following facts are specially important to
understand those differences.
- Many microsatellites detected in our site when percentaje
of allowed mismatches is 0 are not shown at MLVA website; they are included in
a bigger microsatellite obtained when mismatches are allowed. In our
site, a sequence may be included in different microsatellite
repeats when number of mismatches allowed are increased.
- At MLVA website, some microsatellietes with only 2 complete repeated sequences are shown, while minimum number repeats must be at least 3 in our database.
References:
van Belkum A, Scherer S, van Alphen L, Verbrugh H: Short-sequence DNA repeats in prokaryotic genomes. Microbiol Mol Biol Rev 1998, 62:275-93. [PubMed]
Bayliss CD, Dixon KM, Moxon ER. Simple sequence repeats (microsatellites): mutational mechanisms and contributions to bacterial pathogenesis. A meeting review. FEMS Immunol Med Microbiol. 2004 Jan 15;40(1):11-9. [PubMed]
G. Benson, Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Research (1999) 27(2):573-580. [PubMed]
Le Fleche P, Hauck Y, Onteniente L, Prieur A, Denoeud F, Ramisse V, Sylvestre P, Benson G, Ramisse F, Vergnaud G.. A tandem repeats database for bacterial genomes: application to the genotyping of Yersinia pestis and Bacillus anthracis. BMC Microbiol. 2001;1(1):2. [BMC]