ThermoBLAST™ finds all mis-hybridization sites, eliminates false positives in PCR

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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 mis-hybridization 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.

Pcr Assay design tool

Pre-made and customizable genome collections:

  • Human genome
  • Human RefSeq
  • Human microbiome
  • Soil microbes panel
  • Bacterial diversity panel
  • Virus panels
  • Human pathogen panel and etc..

ThermoBLAST Features

(PCR assay design tool)

 ThermoBLAST CEPrimer-BLASTBLAST
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