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ecoPrimers

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 ).
ecoPrimers is a software that finds primers from a set of sequences and is developed by the LECA.
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.
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. The implementation of "agrep" algorithm to find approximate conserved regions to design primers was taken from ecoPCR.

Currently, ecoPrimers is available as a local program that you can download and install on unix-like machine.

Download the archive on this page, then untar it, go into the src directory in the newly created directory, and compile:

tar –zxvf ecoPrimers.tar.gz
cd ecoPrimers/src/
make

You can find the documentation here.