Table 1 Comparison of JCVI Primer Design Tool versus other recently published primer design packages.
From: Novel computational methods for increasing PCR primer design effectiveness in directed sequencing
Feature/Software | Primer Design Assistant (PDA)3 | SNPbox5 | MutScreener6 | EasyExon Primer7 | PrimerZ8 | JCVI Primer Design Tool | |
|---|---|---|---|---|---|---|---|
Year | 2003 | 2005 | 2006 | 2006 | 2007 | 2008 | |
Inputs | Ensembl ID | - | - | - | - | ∗ | ∗ |
DbSNP/AFFY Probe ID | - | - | - | - | dbSNP/AFFY Probe ID | dbSNP ID | |
Genomic coordinates | - | - | UCSC annotation | - | - | Ensembl coordinates | |
RefSeq ID/Genbank ID | - | Genbank ID | - | Refseq mRNA ID | - | - | |
Sequence | ∗ | ∗ | ∗ | - | - | ∗ | |
Primer design parameters validated in lab | - | - | - | ∗ | - | ∗ | |
Allows variable depth of coverage | - | - | - | - | - | ∗ | |
Provides graphical web interface | ∗ | ∗ | ∗ | ∗ | ∗ | - | |
Performs dynamic amplicon tiling | - | ‡ | ‡ | ‡ | ‡ | ∗ | |
Uses available annotation in primer design | - | ∗ | ∗ | ∗ | ∗ | ∗ | |
Checks for stem-loop structures | ∗ | - | - | - | - | ∗ | |
Detects phase shifting events in amplicon | - | stutter only | - | - | - | ∗ | |
Can specify regions to avoid designing primers | - | - | - | - | - | ∗ | |
Check for alternative amplification | - | - | - | ∗†| - | ∗ | |
Enables high-throughput runs | - | ∗ | - | - | - | ∗ | |