ecopcr
estimate PCR barcode primers quality
Command lineScience
Not tested on a device yet. What that means
Commands in the package
ecoPCRecoPCRFilterecoPCRFormatecoSortecofindecogrepecoisundertaxon
About ecopcr
From Debian's package description
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
From Debian's description of the ecopcr package, under that package's license.
Dependencies
Depends on
libc6zlib1gpython3python3-reportlab
Related apps
- reliontoolkit for 3D reconstructions in cryo-electron microscopyCommand line
- pycoqccomputes metrics and generates Interactive QC plotsCommand line
- mipeTools to store PCR-derived dataCommand line
- ncbi-epcrTool to test a DNA sequence for the presence of sequence tagged sitesCommand line
- flexbarflexible barcode and adapter removal for sequencing platformsCommand line
- ampliconnoiseremoval of noise from 454 sequenced PCR ampliconsCommand line
Sources and licenses
- Name: the Debian package name.
- Summary: Debian's short description of the ecopcr package, under that package's license.
- Description: Debian's description of the ecopcr package, under that package's license.
- Versions and sizes: Debian's archive for ARM64, as on packages.debian.org.
- Popularity: Debian Popularity Contest counts.
More in About the catalog.