Oligotyping is the process of correcting
DNA sequence measured during the process of
DNA sequencing based on frequency data of related sequences across related samples.
History
DNA sequences were originally read from sequencing gels by eye. With the advent of computerized base callers, humans no longer 'called' the bases and instead 'corrected' the called bases. The bases were called by the software using the relative intensity of each putative basepair signal and the local spacing of the signals.
With the advent of
high throughput sequencing
DNA sequencing is the process of determining the nucleic acid sequence – the order of nucleotides in DNA. It includes any method or technology that is used to determine the order of the four bases: adenine, guanine, cytosine, and thymine ...
, the volume of sequence to be corrected exceeded human capacity for sequence correction.
Use
Multiple applications require single-base pair accuracy across populations of closely related sequences. An example is
amplicon
In molecular biology, an amplicon is a piece of DNA or RNA that is the source and/or product of amplification or replication events. It can be formed artificially, using various methods including polymerase chain reactions (PCR) or ligase chain ...
sequencing to assess the relative contribution of DNA from diverse organisms to a sample.
The requirement for single basepair accuracy led to the development of methods which drew on frequency data distributed across several samples to identify variant sequences which shared the same frequency profile and were thus likely errors from the same original sequence.
The ability to use higher-order statistics to correct sequences is an important element in decreasing the burden of error in DNA sequence datasets.
See also
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DNA sequencing theory
DNA sequencing theory is the broad body of work that attempts to lay analytical foundations for determining the order of specific nucleotides in a sequence of DNA, otherwise known as DNA sequencing. The practical aspects revolve around designing ...
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DNA sequencer
A DNA sequencer is a scientific instrument used to automate the DNA sequencing process. Given a sample of DNA, a DNA sequencer is used to determine the order of the four bases: G (guanine), C (cytosine), A ( adenine) and T (thymine). This is t ...
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Oligotyping (taxonomy)
Oligotyping is a diagnostic or molecular biological method for classification of organisms by short intervals of primary DNA sequence.
Oligotyping 'systems' are sets of recognized target sequences which identify the members of the categories wit ...
References
External links
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''Next Generation Sequencing (NGS) — ''a wikibook on next generation sequencing''.
Omictools.com: Didactic directory for DNA sequencing analysis (free)
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DNA sequencing
Molecular biology techniques