# Primer Nomenclature

The following is a description of the nomenclature for primers and other sequences that are used in the PaintSHOP probe design application.

Each name has the format: set_type#

For example: ps_of1 is the first outer forward primer of the PaintSHOP set.

## Sets

ps = PaintSHOP
saber_1x = [SABER](http://saber.fish/) PER primers
saber_2x = [SABER](http://saber.fish/) PER primers with two copies of a given concatemer
merfish = Sets from [MERFISH site](http://zhuang.harvard.edu/merfish.html)
Mateo2019 = Sets from [Mateo et al. 2019](https://www.nature.com/articles/s41586-019-1035-4)
Xia2019 = Sets from [Xia et al. 2019](https://www.pnas.org/content/116/39/19490)

## types

of = outer forward primer
or = outer reverse primer

if = inner forward primer
ir = inner reverse primer

primer = primer with no specified forward/reverse
bridge = bridge set that can be used on either 5' or 3' side or used to make a custom set