| Online Tool | Description |
|---|---|
| Dicer-Substrate siRNA | Generates DsiRNAs for any sequence from any species. |
| Genomic Primers | Input form for creating primers around exons in genomic DNA. For primer design, the Primer3 program is used. |
| 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. |
| Primer Design: Uses Primer3-py package | Primer design and sets for amplifying yeast ORFs. |
| Primer-BLAST | Finding primers specific to PCR template (using Primer3 and BLAST). |
| Primer1 | Primer design for tetra-primer ARMS-PCR. PCR designer for restriction analysis of sequence mutations. |
| 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. |
| RF-Cloning | Online tool for the design of primers for restriction-free cloning projects. |
| SFOLD | Software for Statistical Folding of Nucleic Acids and Studies of Regulatory RNAs |
| UCSC In-Silico PCR | In-Silico PCR searches a genome sequence database with a given pair of PCR primers. |
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)