ThermoBLAST™ finds all mishybridization sites, eliminates false positives in PCR

ThermoBLAST™ (Pcr assay design tool) automatically scans oligos against large genome databases to detect all thermodynamically stable hits. Different from BLAST, ThermoBLAST™ captures the important mishybridization hits by considering the following:

  • Appropriate thermodynamic scoring, as BLAST doesn’t differentiate a GC pair from an AT pair
  • Displays all false amplicons
  • Consideration for 3’ extensibility and stable mismatches
  • ThermoBLAST will score based on complementarity as opposed to similarity in BLAST
  • ThermoBLAST allows for solution conditions, salt, buffers, additives and other experimental factors

The more primers that are present in an assay, the higher the chance that a false amplicon could be generated. Thus, multiplexed assays are particularly susceptible to false positives.

Pre-made and customizable genome collections

We maintain a huge repository of curated and pre-formatted sequence databases that can further be arranged into a customized sequence playlist.

Pcr Assay Design Tool

ThermoBLAST Features

(PCR assay design tool)

Single Genome Scan
Multiple Genome Scan
Playlist of Genomes
Detects Extensible Hits
Detects Probe Hybrdization
Evaluates probe dyes and minor groove binders.
Specificity Checking
Sensitivity Checking
Correctly scores mismatches by identity
Detects Amplicons
Adjustable primer extensibility settings
Allows download of amplicon plus tails
Graphic overview of results
Genome view provides detailed thermodynamics
Multiplex Capability
Differentiates DNA from RNA backbones
Modified Backbones
Modified Bases
Uses Monovalent Salt
Uses Divalent Salt
Simulates at different temperatures
Simulates at different primer concentrations
Correctly scores target dangling ends
Correctly scores bulges