Why you Shouldn’t use BLAST

BLAST isn’t “free” when you consider hidden costs such as lost time and higher reagent costs due to the need to redesign primers and probes.

Advantages of ThermoBLAST and probe synthesis and optimization with BLAST can become expensive due to a few core limitations:

  • Hits are scored on sequence similarity rather than thermodynamic affinity
  • Simulation is not possible under actual experimental oligonucleotide concentrations and salt conditions
  • False amplicons and off-target effects cannot be quantified
  • DNA/DNA, RNA/RNA, or DNA/RNA hybrid duplexes cannot be properly scored for basepair matches or mismatch geometry
  • Oligonucleotide secondary structure motifs including bulges, mismatches and dangling ends, are properly accounted for
  • Modified nucleotides and backbones are completely ignored