ThermoBLAST TM Genome Scanning Software
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Overview:
Better than BLAST for checking assay designs. Scans entire genomes quickly and accurately combing the speed of BLAST with the most advanced thermodynamics parameters of OMPTM. Ensures that your probes/primers do not mis-hybrize to unintended targets. Eliminates all potential assay false positives and negatives. Exceptionally sensitive and specific.
ThermoBLASTTM Superior to BLAST:
BLAST was originally designed for evolutionary applications and not for checking probe/primer designs. BLAST is limited to only exact-match base pairing (i.e. A:T and G: C) for all word sizes. Furthermore, BLAST contains a minimum word size restriction of 7 nucleotides. In contrast, ThermoBLASTTM accounts for actual hybridization for both matches and mismatches, including mismatches that are stabilizing (e.g. G:G, G:T, A:G, etc.) as well as deletions, loops, bulges, etc. Moreover, it has the ability to discern and quantify nonspecific binding to a single base pair mutation at the genome scale. ThermoBLASTTM accounts for temperature and salt concentrations. In addition, it provides a quick primer screening option and reports if hits can be extended by DNA polymerase. ThermoBLASTTM ranks mishybridization hits; generates thermodynamic and Tm values; and shows secondary structures for each hit.
A more detailed summary of ThermoBLASTTM versus BLAST can be found in our publication on Optimal PCR Design.
Accurate:
ThermoBLASTTM with its affinity rather than similarity approach picks up 100% of actual hybridizations (very sensitive) and eliminates all false positives (very specific). In an NIH sponsored study, DNA Software compared BLAST with ThermoBLASTTM by querying one sequence against 25 different human, yeast, and bacterial chromosomal targets. DNA Software found that on average BLAST only picked up about 11% of actual thermodynamic hits (actual hybridizations) and had a false positive rate of about 18% (higher than 50% in some cases). Whereas, ThermoBLASTTM picked up 100% of actual hits and had a false positive rate of 0%.
ThermoBLASTTM is powered by the advanced thermodynamics of DNA Software's OMPTM engine, which contains the industry’s largest database of thermodynamic parameters. DNA Software has conducted thousands of diverse nucleic acid melt experiments to derive and validate its thermodynamic parameters. Thus, ThermoBLASTTM’s predictions are backed by experimental data and are exceptionally accurate.
DNA, RNA, and Modified Nucleotides:
ThermoBLASTTM allows users to simultaneously query multiple DNA or RNA sequences against large databases containing DNA or RNA targets. Thus, in addition to DNA-DNA, ThermoBLASTTM can search for RNA-RNA, DNA-RNA, or RNA-DNA hybridizations. DNA Software offers an additional option to add modified nucleotides (e.g. LNA, PNA, Morpholinos, plus many more) to ThermoBLASTTM.
Features:
· Searches can be run on genome targets in seconds. Benchmark of 1 million base pairs runs in < 3 seconds.
· Ability to discern and quantify nonspecific binding to a single base pair mutation at the genome scale.
· Ability to indicate if a hybridization is likely to be extended by DNA Polymerase.
· Quick Primer Screening: ability to only check the 3'-end of PCR primers for significant hybridizations.
· Takes differing solution conditions into account.
· Ability for user to set thermodynamic thresholds to determine if a hit is significant or not.
Product Options:
ThermoBLASTTM is offered in two different product formats. It is available as an additional module that integrates into Visual OMPTM (for Windows systems), or as a customizable command line driven application for high-throughput analysis and computer clusters (for Linux or Windows systems).
The best way to learn how ThermoBLASTTM can assist your work is to schedule a live web demo specifically tailored to your research interests.
Paradigm-shifting Technology for Assay Development:
ThermoBLASTTM is the optimal tool for checking assay designs. It combines the speed of BLAST with the advanced thermodynamics of OMP to quickly and accurately check probes and primers against whole genomes. Moreover, it identifies potential mishybridizations to unintended targets and determines if such false positives are extensible by DNA polymerase.
ThermoBLASTTM builds on years of research and development to use affinity rather than similarity to convincingly determine all possible nucleic acid interactions and to detect false positives and negatives. Furthermore, ThermoBLASTTM can be adjusted to account for differences in assay temperature, salt conditions, and oligo concentrations among other factors to produce unbelievably accurate results tailor made for any nucleic acid based technology.
ThermoBLASTTM is an efficiency technology that all scientists should consider utilizing while developing their assays. It will eliminate all false positives and negatives, design the most sensitive and selective assays, and save organizations significant time, money, and resources.
Leading Research Organizations Use ThermoBLASTTM:
DNA Software has many prominent customers in the diagnostic, biodefense, and biotech industries as well as in academia and government. Many research projects around the world are benefitting from the power and accuracy of ThermoBLASTTM. In addition to improving assays and diagnostics, ThermoBLASTTM can be applied to address the significant problem of false positives in bio-threat detection. DNA Software has a contract with the Department of Homeland Security (DHS) to apply the ThermoBLASTTM technology.
The Centers for Disease Control and Prevention (CDC), the U.S. Army Medical Research Institute of Infectious Diseases (USAMRIID), and Harvard University utilize DNA Software’s products and have published on the application of Visual OMPTM and OMP Developer EditionTM. These CDC, USARIID, and Harvard references plus many others can be found on DNA Software’s Testimonial & Acknowledgments web page.
ThermoBLASTTM Support & Training