ThermonucleotideBLAST is an application for searching a target database of nucleic acid sequences using an assay specific query that is 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 like BLAST, which use heuristic measures of sequence similarity for identifying matches between a query and target sequence, ThermonucleotideBLAST uses free energy and melting temperature.
What's New in This Release:
· This update features a significant rewrite of thermodynamic alignment algorithm, including the addition of the Dinkelbach fractional programming algorithm for computing duplex melting temperatures.