Scans multiple primers against collections of genomes to find all hybridizations and amplicons.

ThermoBLAST finds all mishybridization sites, eliminates false positives in PCR

Solving Primer Specificity

ThermoBLAST™ 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
Pcr Assay Design Tool

The problem of false positives in PCR

The most common cause of false positives in PCR is the formation of false amplicons due to primer mishybridization which is not detected by BLAST because it scores hits incorrectly using sequence similarity rather than using the proper rules for match and mismatch complementarity.   Additionally, many researchers do not have access to the computational capacity or storage required of modern genomic-based assay designs.

The solution to false positives in PCR

ThermoBLAST CE and ThermoBLAST solves the problem of primer and probe mishybridization by scanning against whole genome databases such as the human genome or microbiome using the speed of BLAST while applying the proper thermodynamic model to mishybridization and crosshybridization results.   The cloud integration of ThermoBLAST CE enables all researchers with the computational power to capture 50X as many thermodynamically stable and extensible hits as BLAST.

How to Eliminate False Positive in PCR Design.

Pre-made and customizable genome collections

ThermoBLAST-CE contains a huge repository of curated and pre-formatted sequence databases that can further be arranged into a customized sequence playlist. Some of the most popular playlists are shown below. Customers now have the capability to build a background database as large as they need without restricting memory, storage or computational capacity which is a huge source of pain for those researchers that have limited local computational capacity.

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

“In my experience, DNA Software™ saved me 75% of my oligo costs.”

Helen Minnis, Wave 80

Interested in learning more about ThermoBLAST™?

ThermoBLAST finds all mishybridization sites, eliminates false positives in PCR. See how ThermoBLAST™ can benefit your organization.