TNTBLAST

Description

tntblast website

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. Installed versions: tntblast === single core tntblastomp === OpenMP tntblastompncbi === OpenMP + ncbi tntblastompncbiunaf === OpenMP + ncbi + unafold

Environment Modules

Run module spider tntblast to find out what environment modules are available for this application.

Environment Variables

• HPC_TNTBLAST_DIR - installation directory
• HPC_TNTBLAST_BIN - executable directory

Categories

biology