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Europe PubMed Central
Other literature type . 2005
Data sources: PubMed Central
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Philosophical Transactions of the Royal Society B Biological Sciences
Article . 2005 . Peer-reviewed
License: Royal Society Data Sharing and Accessibility
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Microcoding: the second step in DNA barcoding

Authors: R C, Summerbell; C A, Lévesque; K A, Seifert; M, Bovers; J W, Fell; M R, Diaz; T, Boekhout; +3 Authors

Microcoding: the second step in DNA barcoding

Abstract

After the process of DNA barcoding has become well advanced in a group of organisms, as it has in the economically important fungi, the question then arises as to whether shorter and literally more barcode-like DNA segments should be utilized to facilitate rapid identification and, where applicable, detection. Through appropriate software analysis of typical full-length barcodes (generally over 500 base pairs long), uniquely distinctive oligonucleotide ‘microcodes’ of less than 25 bp can be found that allow rapid identification of circa 100–200 species on various array-like platforms. Microarrays can in principle fulfill the function of microcode-based species identification but, because of their high cost and low level of reusability, they tend to be less cost-effective. Two alternative platforms in current use in fungal identification are reusable nylon-based macroarrays and the Luminex system of specific, colour-coded DNA detection beads analysed by means of a flow cytometer. When the most efficient means of rapid barcode-based species identification is sought, a choice can be made either for one of these methodologies or for basic high-throughput sequencing, depending on the strategic outlook of the investigator and on current costs. Arrays and functionally similar platforms may have a particular advantage when a biologically complex material such as soil or a human respiratory secretion sample is analysed to give a census of relevant species present.

Country
Netherlands
Subjects by Vocabulary

Microsoft Academic Graph classification: Base pair Sample (material) Computational biology Biology Barcode Bioinformatics DNA barcoding law.invention law Software analysis pattern Oligonucleotide Identification (biology) DNA microarray

Keywords

Oligonucleotides, yeasts, mycobacterium-tuberculosis, phylogeny, General Biochemistry, Genetics and Molecular Biology, Species Specificity, systematics, hybridization, Electronic Data Processing, EPS-4, Biodiversity, DNA, differentiation, Flow Cytometry, Microarray Analysis, Laboratorium voor Phytopathologie, Molecular Diagnostic Techniques, Laboratory of Phytopathology, identification, fungi, molecular taxonomy, General Agricultural and Biological Sciences, complex, Research Article

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    Top 10%
    influence
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    Top 10%
    impulse
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    Top 10%
  • citations
    This is an alternative to the "Influence" indicator, which also reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
    95
    popularity
    This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network.
    Top 10%
    influence
    This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
    Top 10%
    impulse
    This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.
    Top 10%
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citations
This is an alternative to the "Influence" indicator, which also reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Citations provided by BIP!
popularity
This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network.
BIP!Popularity provided by BIP!
influence
This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Influence provided by BIP!
impulse
This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.
BIP!Impulse provided by BIP!
95
Top 10%
Top 10%
Top 10%
Green
bronze