- 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 ).
ecoPCR is an electronic PCR software developed by the LECA. It helps you estimate Barcode primers quality. In conjunction with OBITools, you can postprocess ecoPCR output to compute barcode coverage and barcode specificity. New barcode primers can be developed using the
ecoPCR is available as a local program that you can download and install on unix-like machines.
Download the archive on this page, then untar it, go into the src directory in the newly created directory, and compile:
tar -zxvf ecopcr-*.tar.gz cd ecoPCR/src/ make
You can then run
ecoPCR and print the help with:
You can find the documentation here.