ThermoBLAST^™

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

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.

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)