Full genome testing

Now it is possible to test primer pairs against the full genome for some annotations (marked with genome+ in the annotation dropdown). This means that also intergenic regions will be searched for possible amplicons; in the normal case only annotated gene/pseudogene loci would be searched.

This option can be activated in custom primer specificity testing parameter sets - on the "Create new project" page, select "Custom" as quantification protocol and create your own primer pair design and specificity testing parameters. Full genome testing is then performed on all primer pairs which pass cDNA and (gene model) gDNA specificity tests.

We recommend to use this option only for poorly annotated or freshly sequenced genomes. On well-annotated genomes (e.g. Arabidopsis thaliana) you will get a noticable performance drop (3-4 times slower testing) without any benefits (meaning additional amplicons not detected by the standard search of gene model sequences) - at least in our preliminary tests on a few hundreds of genes. On newly sequenced genomes, such as Physcomitrella patens, we noticed an improved detection of genomic amplicons for less than one out of hundred genes.


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