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 LECA ( 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.

Documentation

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Download preformated DB