[Bioclusters] Announcing ThermonucleotideBLAST

Jason Gans jgans at lanl.gov
Tue Nov 27 15:21:51 EST 2007

ThermonucleotideBLAST is a software program for searching a target 
database of nucleic acid sequences using queries based biochemical 
assays (i.e. a pair of oligonucleotide sequences representing PCR 
primers or Padlock probes, a triplet of oligos representing PCR primers 
and a TaqMan probe or a single oligo representing a hybridization 

ThermonucleotideBLAST uses physically relevant measures of sequence 
similarity (free energy and/or melting temperature) to identify matches 
between a query and target sequence.

To enable searching of very large sequence databases, 
ThermonucleotideBLAST uses run-time database and query segmentation to 
distribute the computational load across multiple CPUs (using either 
MPI or OpenMP). Supported platforms include Linux, OS X and Windows.

The source code is freely available (BSD license) from 


Jason Gans

Bioscience Division
Los Alamos National Laboratory

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