| Online Tool | Description |
|---|---|
| AutoPrime | Primer design for real-time PCR measurement of eukaryotic gene expression. |
| CODEHOP | COnsensus-DEgenerate Hybrid Oligonucleotide Primers designed from protein multiple sequence alignments. |
| ExonPrimer | Design intronic primers for PCR amplification of exons. Input needed: a cDNA and the corresponding genomic sequence. |
| IDT AntiSense Design | Antisense oligo design and selection tool. |
| IDT Oligo Analyzer | Online calculation of oligonucleotide parameters such as melting temperature. Shows self-dimers, hairpin, and performs Blast. |
| IDT PrimerQuest | Primer and probe design and selection. |
| NetPrimer | Java applet for primer design. |
| Oligonucleotide Analyzer | Generates Tm, free energy, molecular weight and hairpin and dimer formation structures. |
| Primer3 | Utility for locating oligonucleotide primers for PCR amplification of DNA sequences. |
| PrimerX | Automated design of mutagenic primers for site-directed mutagenesis. |
| Primo Pro | PCR Primer Design. |
| QuantPrime | Automatic high-throughput primer pair design and specificity testing for realtime qPCR on any organism. |
| RNAi Design | Design duplexed RNA oligos for RNA interference. |
| SiteFind | Design of oligonucleotide primers for site-directed-mutageneis that include a novel restriction for use as a marker of successful mutation. |
| UCSC In-Silico PCR | In-Silico PCR searches a genome sequence database with a given pair of PCR primers. |
| Web Primer | Primer design and sets for amplifying yeast ORFs. |
Primer Design Considerations
Desired characteristics of automated DNA sequencing primer design.
- Based on accurate sequence
- Melting temperature (Tm): 52°C to 65°C
- Absence of self-hybridization
- Absence of significant hairpin formation (>3 bp)
- Lack of secondary priming sites
- Low specific binding at the 3' end (ie. lower GC content to avoid mispriming)
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