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Primer & Probe Design Tools

  • Oligo
OLIGO helps researchers to design oligonucleotides primers/probes used for PCR reaction, DNA sequencing, site-directed mutagenesis, and various hybridization applications. Primers/probes are designed based on a set of well-accepted criteria. In case that no perfect primers/probes identified, it allows user to choose some optimal oligonucleotide sequences and report the biochemical features of them, such as delta-G profile, hybridization temperature, possible secondary structure, and so on. It is also a good tool for construction of synthetic genes, finding an appropriate sequencing primer among those already synthesized, finding and multiplexing consensus primers and probes, and even finding potential restriction sites in a protein.

  • Primer3
Primer3 is a complete rewrite of the original PRIMER program.Primer3 picks primers for PCR reactions, considering as criteria:

  Oligonucleotide melting temperature, size, GC content,
  Primer-dimer possibilities,
  PCR product size,
  Positional constraints within the source sequence, and
  Miscellaneous other constraints.

All of these criteria are user-specifiable as constraints, and some are specifiable as terms in an objective function that characterizes an optimal primer pair.

  • Melting Temperature Calculation Tools (BioMath)
Melting Temperature (Tm) is a very important feature for primers/probes. Currently, there're three algorithms used for Tm calculation. Each has different application field. Tms calculated using these three algorithms sometimes give similar results, sometimes gives temperature with big differences. BioMath provides a good Tm calculation service that gives results using all three algorithms