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- DNA barcoding is a tool for characterizing the species origin using
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a short sequence
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a short sequence from a standard position and agreed upon position
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in the genome. To be used as a DNA barcode, a genome locus should
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vary among individuals of the same species only to a minor degree
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and it should vary among species very quickly. From a practical
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point of view, a barcode locus should be flanked by two conserved
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regions to design PCR primers. Several manually discovered barcode
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loci like COI, rbcL, 18S, 16S and 23S rDNA, or trnH-ps are routinely
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used today, but no objective function has been described to measure
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their quality in terms of universality (barcode coverage, Bc ) or in
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terms of taxonomical discrimination capacity (barcode specificity,
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Bs ).
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` from a standard position and agreed upon position in the genome. To be used as a DNA barcode, `\
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` a genome locus should vary among individuals of the same species only to a minor degree and it `\
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` should vary among species very quickly. From a practical point of view, a barcode locus should be `\
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` flanked by two conserved regions to design PCR primers. Several manually discovered `\
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` barcode loci like COI, rbcL, 18S, 16S and 23S rDNA, or trnH-ps are routinely used today, but no `\
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` objective function has been described to measure their `\
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` quality in terms of universality (barcode coverage, Bc ) or in terms of taxonomical discrimination `\
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` capacity (barcode specificity, Bs ). `
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\`ecoPCR\` is an electronic PCR software developed by LECA
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([LECA](http://www-leca.ujf-grenoble.fr/)) and Helix-Project
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([HELIX](http://www.inria.fr/recherche/equipes/helix.fr.html)). It helps
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you to estimate Barcode primers quality. In conjunction with
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[OBITools](http://www.grenoble.prabi.fr/trac/OBITools) you can
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postprocess ecoPCR output to compute barcode coverage and barcode
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specificity. New barcode primers can be developed using the
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[ecoPrimers](http://www.grenoble.prabi.fr/trac/ecoPrimers)
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software[BR](BR "wikilink")
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*`ecoPCR`*` is an electronic PCR software developed by LECA (`[`LECA`](http://www-leca.ujf-grenoble.fr/)`) and Helix-Project (`[`HELIX`](http://www.inria.fr/recherche/equipes/helix.fr.html)`). It helps you to estimate Barcode primers quality. In conjunction with `[`OBITools`](http://www.grenoble.prabi.fr/trac/OBITools)` you can postprocess ecoPCR output to compute barcode coverage and barcode specificity.`\
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`New barcode primers can be developed using the `[`ecoPrimers`](http://www.grenoble.prabi.fr/trac/ecoPrimers)` software`[`BR`](BR "wikilink")\
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\
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`Currently, ecoPCR is available as a local program that you can download and install on unix like machine.`
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Currently, ecoPCR is available as a local program that you can download and
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install on unix like machine.
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[ecoPrimers](http://www.grenoble.prabi.fr/trac/ecoPrimers)
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