TNTBLAST
Description
TNTBLAST (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 TaqManTM probe or a single oligo representing a hybridization probe). Unlike existing programs (e.g. 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.
Environment Modules
Run module spider TNTBLAST to find out what environment modules are available for this application.
System Variables
- HPC_TNTBLAST_DIR - installation directory