GeneMarker^® for Amplified Fragment Length Polymorphisms (AFLP ®*)

GeneMarker for AFLP is a “biologist-friendly” software tool designed to make analysis efficient, quick, and easy. The software automatically corrects for common PCR-related problems such as saturated peaks, instrument spikes, and stutter peaks. GeneMarker successfully identifies allelic differences between closely related species by using a direct trace comparison of sample to reference. The user is able to save and print multiple reports including an AFLP report displaying the presence, absence, and questionable presence of alleles and a trace comparison report which displays allelic differences between sample traces and a user-defined reference trace.

AFLP Report AFLP Intensity Report

The software has an AFLP Report which displays the presence (1), absence (0), and questionable presence (?) of alleles. Alleles with a score above the specified “Pass” threshold in the Run Wizard will be labeled 1 with a green flag. Alleles which fall in the “Check” range will be represented by a question mark and yellow symbol. Cells which contain a zero have either no allele detected or the allele is below the “Reject” threshold. Alleles with a red symbol fall outside the panel range for that allele. This report can be saved as a text file to be imported into Excel for printing.

The user may display the peak intensity in the AFLP report as opposed to the presence/absence of alleles. In this report option, each cell representing a detected allele contains the intensity value for that peak. The symbols remain the same as in the regular AFLP report and this report may also be saved as a text file.

Trace Comparison Report Print AFLP Report

The Trace Comparison function for AFLP Analysis compares the presence and/or absence of allele peaks between closely related species. The allelic differences are based upon Poisson differentiation where a user-defined reference is compared to the sample traces at the position of each detected allele.

The printing options for AFLP include a choice to print all or selected samples, the electropherogram and/or peak table, and one, all, or a mixture of dyes. The user may also print each sample on a different page, label dyes and peak numbers, or print project commands.

Application Notes

AFLP Application Note [pdf]

*AFLP is a registered trademark of KeyGene, N.V.

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