Table 2 Algorithm parameters and default values other than for primer/probe design
From: barCoder: a tool to generate unique, orthogonal genetic tags for qPCR detection
Purpose | Parameter description | Default values |
|---|---|---|
Spacer size | Total spacer size (bases between forward/reverse primers, inclusive of probe but not of forward/reverse primers) | 100 |
Full barcode Module stem-loops | Minimum stem-loop hydrogen bonds | 14 |
Minimum stem-loop palindrome length (bases) | 10 | |
Maximum stem-loop palindrome length (bases) | 80 | |
Maximum stem-loop gap size (bases) | 11 | |
Maximum stem-loop mismatches | 1 |