"Classification and review of free PCR primer design software"
Jingwen Guo, David Starr, and Huazhang Guo
Primer3
| Publications | Availability | Interface | Language | |
|---|---|---|---|---|
| Primer3 | Rozen and Skaletsky, Koressaar and Remm, Untergasser et al. |
Open | WUI/CUI | C |
Sanger
| Publication | Availability | Primer3-Based? | Interface | Language | |
|---|---|---|---|---|---|
| PrimerZ | Tsai et al. | Free | Yes | WUI | Java |
| JCVI Primer Designer | Li et al. | Open | No | CUI | Perl |
| ExonPrimer | N/P | Free | Yes | WUI | Perl |
| MPDP3 (abbr.) | N/P | Free | Yes | WUI | ? |
| ConservedPrimer2.0 | You et al. | Open | Yes | WUI/CUI | Java |
| PrimerDesign-M | Yoon and Leitner | Free | No | WUI | ? |
RT-qPCR
| Publication | Availability | Primer3-Based? | Interface | Language | |
|---|---|---|---|---|---|
| AutoPrime | Wrobel et al. | Open | Yes | WUI | Perl |
| QuantPrime | Arvidsson et al. | Free | Yes | WUI | Python/PHP |
| Primer-BLAST | Ye et al. | Open | Yes | WUI | C++ |
SNP
| Publication | Availability | Primer3-Based? | Interface | Language | |
|---|---|---|---|---|---|
| PIRA PCR designer | Ke et al. | Free | No | WUI | Java |
| PRIMER1 | Ye | Free | No | WUI | Java |
| PCR designer | Ke et al. | Free | No | WUI | ? |
Splicing Variant
| Publication | Availability | Primer3-Based? | Interface | Language | |
|---|---|---|---|---|---|
| RASE | Brosseau et al. | Free | Yes | WUI | Perl |
| PRIMEGENS-v2 | Srivastava et al. | Open | Yes | WUI/CUI | C |
| PrimerSeq | Tokheim et al. | Open | Yes | GUI | Java |
Methylation
| Publication | Availability | Primer3-Based? | Interface | Language | |
|---|---|---|---|---|---|
| Methprimer | Li and Dahiya | Free | Yes | WUI | C/Perl |
| BiSearch | Tusnady et al. | Free | No | WUI | ? |
| Bisprimer | Kovacova and Janousek | Free | No | GUI | ? |
| MSP-HTPrimer | Pandey et al. | Open | Yes | WUI | Python |
Microsatellite
| Publication | Availability | Primer3-Based? | Interface | Language | |
|---|---|---|---|---|---|
| MSATCOMMANDER | Faircloth | Open | Yes | CUI/GUI | Python |
| WebSat | Martins et al. | Free | Yes | WUI | Javascript/PHP |
| QDD | Meglécz et al. | Free | Yes | CUI/Galaxy | Perl |
Conserved/ Degenerate
| Publication | Availability | Primer3-Based? | Interface | Language | |
|---|---|---|---|---|---|
| HYDEN | Linhart and Shamir | Free | No | CUI | C++ |
| Amplicon | Jarman | Open | No | GUI | Python |
| Primaclade | Gadberry et al. | Free | Yes | WUI | Bioperl |
| PriFi | Fredslund et al. | Free | No | WUI | ? |
| GeneFisher2 | Lamprecht et al. | Free | No | WUI | Javascript/XML |
| PrimerIdent | Pessoa et al. | Free | Yes | WUI | Perl |
| TOPSI | Vijaya Satya et al. | Open | Yes | WUI/CUI | BioPerl |
| Gemi | Sobhy and Colson | Open | Yes | GUI | C# |
| easyPAC | Rosenkranz | Free | No | CUI | Perl |
Multiplex
| Publication | Availability | Primer3-Based? | Interface | Language | |
|---|---|---|---|---|---|
| MultiPLX | Kaplinski and Remm | Free | No | CUI/WUI | C++ |
| MuPlex | Rachlin et al. | Free | No | WUI | Java |
| PrimerStation | Yamada et al. | Free | No | WUI | ? |
| MPprimer | Shen et al. | Open | Yes | CUI/WUI | Python |
| Optimus Primer | Brown et al. | Free | Yes | WUI | ? |
| MCMC-ODPR | Kitchen et al. | Free | No | CUI | Perl/Java |
| MPD | Wingo et al. | Open | No | WUI/CUI | C/Perl |
| Oli2go | Hendling et al. | Free | Yes | WUI | Python |
Multifunctional
| Publication | Availability | Primer3-Based? | Interface | Language | |
|---|---|---|---|---|---|
| Primo | Li et al. | Free | No | WUI | C |
| PerlPrimer | Marshall | Open | No | GUI | Perl/TK |
| The PCR suite | Baren and Heutink | Open | Yes | WUI | Perl |
| BatchPrimer3 | You et al. | Free | Yes | WUI | Perl |
| jPCR | Kalendar et al. | Free | No | GUI | Java |
Niche Applications
| Function | Publication | Availability | Primer3-Based? | Interface | Language | |
|---|---|---|---|---|---|---|
| RJPrimers | Transposon | You et al. | Open | Yes | WUI/CUI | Perl/Java |
| PrimerX | Mutagenesis | N/P | Free | ? | WUI | ? |
| AcePrimer | C. elegans | Mckay and Jones | Free | Yes | WUI | Perl |
| PrecisePrimer | Cloning | Pauthenier and Faulon | Free | No | WUI | ? |
| MultiMPrimer3 | Pathogen | Koressaar et al. | Free | Yes | WUI | Perl |
| AmplifX | Management | N/P | Free | No | GUI | ? |