Sequence-tagged site
Encyclopedia
A sequence-tagged site is a short (200 to 500 base pair) DNA
sequence that has a single occurrence in the genome
and whose location and base sequence are known.
STSs can be easily detected by the polymerase chain reaction
(PCR) using specific primer
s. For this reason they are useful for constructing genetic and physical maps from sequence data reported from many different laboratories. They serve as landmarks on the developing physical map of a genome.
When STS loci
contain genetic polymorphisms (e.g. simple sequence length polymorphisms, SSLPs, single nucleotide polymorphisms), they become valuable genetic markers, i.e. loci which can be used to distinguish individuals.
They are used in shotgun sequencing
, specifically to aid sequence assembly
.
STSs are very helpful for detecting microdeletions in some genes for example some STSs can screening by pcr to detecting microdeletions in azf genes in infertile men.
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...
sequence that has a single occurrence in the genome
Genome
In modern molecular biology and genetics, the genome is the entirety of an organism's hereditary information. It is encoded either in DNA or, for many types of virus, in RNA. The genome includes both the genes and the non-coding sequences of the DNA/RNA....
and whose location and base sequence are known.
STSs can be easily detected by the 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....
(PCR) using specific primer
Primer (molecular biology)
A primer is a strand of nucleic acid that serves as a starting point for DNA synthesis. They are required for DNA replication because the enzymes that catalyze this process, DNA polymerases, can only add new nucleotides to an existing strand of DNA...
s. For this reason they are useful for constructing genetic and physical maps from sequence data reported from many different laboratories. They serve as landmarks on the developing physical map of a genome.
When STS 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...
contain genetic polymorphisms (e.g. simple sequence length polymorphisms, SSLPs, single nucleotide polymorphisms), they become valuable genetic markers, i.e. loci which can be used to distinguish individuals.
They are used in shotgun sequencing
Shotgun sequencing
In genetics, shotgun sequencing, also known as shotgun cloning, is a method used for sequencing long DNA strands. It is named by analogy with the rapidly-expanding, quasi-random firing pattern of a shotgun....
, specifically to aid sequence assembly
Sequence assembly
In bioinformatics, sequence assembly refers to aligning and merging fragments of a much longer DNA sequence in order to reconstruct the original sequence. This is needed as DNA sequencing technology cannot read whole genomes in one go, but rather reads small pieces of between 20 and 1000 bases,...
.
STSs are very helpful for detecting microdeletions in some genes for example some STSs can screening by pcr to detecting microdeletions in azf genes in infertile men.