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==========
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- DNA barcoding is a tool for characterizing the species origin using a short sequence from a standard position and agreed upon position in the genome. To be used as a DNA barcode, a genome locus should vary among individuals of the same species only to a minor degree and it should vary among species very quickly. From a practical point of view, a barcode locus should be flanked by two conserved regions to design PCR primers. Several manually discovered barcode loci like COI, rbcL, 18S, 16S and 23S rDNA, or trnH-ps are routinely used today, but no objective function has been described to measure their quality in terms of universality (barcode coverage, Bc ) or in terms of taxonomical discrimination capacity (barcode specificity, Bs ).
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- ecoPrimers is a software that finds primers from a set of sequences and is developed by LECA ([LECA](http://www-leca.ujf-grenoble.fr/)). [BR](BR "wikilink")
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- ecoPrimers is a software that finds primers from a set of sequences and is developed by the [LECA](http://www-leca.ujf-grenoble.fr/).
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- This software is developed by using a more formal approach to qualify a barcode region (Bc , Bs functions) and a new way for identifying barcode loci without a priori on the candidate sequences.
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- Our barcode inferring method is the combination of an algorithm to detect conserved regions from a set of full genome sequences to design PCR primers and objective functions to determine the quality of a barcode locus. The definition of these objective functions are taken from ([OBITools](http://metabacoding.org/obitools)). The implementation of "agrep" algorithm to find approximate conserved regions to design primers was taken from ([ecoPCR](http://metabacoding.org/ecopcr)).
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- Our barcode inferring method is the combination of an algorithm to detect conserved regions from a set of full genome sequences to design PCR primers and objective functions to determine the quality of a barcode locus. The definition of these objective functions are taken from [OBITools](http://metabacoding.org/obitools). The implementation of "agrep" algorithm to find approximate conserved regions to design primers was taken from [ecoPCR](http://metabacoding.org/ecopcr).
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Currently, ecoPrimers is available as a local program that you can download and install on unix like machine.
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Currently, ecoPrimers is available as a local program that you can download and install on unix-like machine.
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[Documentation](http://metabarcoding.org/obitools/doc/scripts/ecoPrimers.html)
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[Download source](https://git.metabarcoding.org/obitools/ecoprimers) |
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## Installing ecoPrimers
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Download the archive on this page, then untar it, go into the src directory in the newly created directory, and compile:
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tar –zxvf ecoPrimers.tar.gz
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cd ecoPrimers/src/
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make
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## Documentation
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You can find the documentation [here](http://metabarcoding.org/obitools/doc/scripts/ecoPrimers.html).
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## See also
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[ecoPCR](https://git.metabarcoding.org/obitools/ecopcr/wikis/home)
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## Download
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[ecoPrimers.tar.gz](https://git.metabarcoding.org/obitools/ecoprimers/uploads/37c37c8d4dd62f53d66dae7a7f7b2318/ecoPrimers.tar.gz)
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