• 1. CODEHOP
• University of Washington. Creates consensus degenerate hybrid oligonucleotide primers from a set of aligned sequences

• 2. Electronic PCR
• NCBI. Real-time Web-based or downloadable code that searches NCBI's STS (sequence tagged site) database for validated forward or reverse primers.

• 3. NCBI Probe Database
• NCBI. Probe Database is a public registry of nucleic acid reagents designed for use in a wide variety of biomedical research applications, together with information on reagent distributors, probe effectiveness, and computed sequence similarities.

• 4. OligoCalc: Oligonucleotide Properties Calculator
• Northwestern. Calculates melting temperatures, thermodynamic constraints and other physical properties for an entered nucleotide sequence.

• 5. Primer3
• MIT. Primer3 is a widely used program for designing PCR primers. Primer3 can also design hybridization probes and sequencing primers.

• 6. ProbeWiz server
• Center for Biological Sequence Analysis. Design PCR primers for amplifying probes for cDNA arrays, with the goal of reducing or eliminating cross-hybridizations

• 7. Projector 2
• MolGen. Projector was designed for automatic positioning of contigs from an unfinished prokaryotic genome onto (parts of) a template genome of a closely related strain or species in order to to close a significant number of remaining gaps in the late stages of a genome sequencing project.

• 8. PUNS: Primer-UniGene Selectivity Testing
• Compares primer sequences against the both the genome and transcriptome to assess the potential for multiple amplicons.

• 9. qPrimerDepot
• NCI.NIH. Provides a searchable database of qRT PCR primers for the sequences in NCBI's RefSeq database.

• 10. Quantitative PCR Primer Database - QPPD
• NIH, NCI. The Quantitative PCR Primer Database (QPPD) provides information about primers and probes that can be used to quantitate human and mouse mRNA by reverse transcription polymerase chain reaction (RT–PCR) assays.

• 11. RTPrimerDB: the real-time PCR primer and probe database
• Ghent University. RTPrimerDB is a public database for primer and probe sequences used in real-time PCR assays employing popular chemistries (SYBR Green I, Taqman, Hybridisation Probes, Molecular Beacon) to prevent time-consuming primer design and experimental optimisation, and to introduce a certain level of uniformity and standardisation among different laboratories.

• 12. SNPbox
• SNPbox is a modular software package that automates the design of PCR primers for large-scale amplification and sequencing projects designed at constructing single nucleotide polymorphism (SNP) maps.