Bug#789921: ITP: ecopcr -- estimate PCR barcode primers quality
Package: wnpp
Severity: wishlist
Owner: Andreas Tille <tille@debian.org>
* Package name : ecopcr
Version : 0.5.0
Upstream Author : Atelier de BioInformatique
* URL : http://www.grenoble.prabi.fr/trac/ecoPCR/
* License : CeCILL_V2
Programming Lang: C, Python
Description : estimate PCR barcode primers quality
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 LECA and
Helix-Project. It helps to 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 ecoPrimers software
The package is maintained by the Debian Med team at
Vcs-Git: git://anonscm.debian.org/debian-med/ecopcr.git
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