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ThermonucleotideBLAST is a software program for searching a target database of nucleic acid sequences using an assay specific query. ThermonucleotideBLAST queries are based on 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 probe). Unlike existing programs (i.e. BLAST) which use heuristic measures of sequence similarity for identifying matches between a query and target sequence, ThermonucleotideBLAST uses physically relevant measures of sequence similarity – free energy and melting temperature. For example, given a pair of PCR primers, a database of DNA targets and an annealing temperature, ThermonucleotideBLAST will return a list of predicted amplicons that will (ideally) match experimental PCR results. To enable searching of very large sequence databases (i.e. all of Genbank), ThermonucleotideBLAST can use run-time database and query segmentation to distribute the computational load across multiple CPUs.
ThermonucleotideBLAST is available, under a BSD Open Source license, from http://snp.lanl.gov/tntblast
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Discussion forums: Software: ThermonucleotideBLAST: Assay specific searching of nucleic acid sequence databases
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