Online tools for PCR, QF-PCR, LAMP, genotyping, electronic PCR, Gibson assembly, primer analysis, setting up reactions, and repeats identification

TotalRepeats

Tool for de novo identification, masking, and clustering of all repeated sequences at the genomic scale. This tool detects DNA sequences with interspersed repeats and low-complexity DNA sequences (simple sequence repeats or microsatellites, telomers, and satellite sequences).

In silico PCR tool

Virtual (in silico) or electronic PCR (ePCR) primers/probes or microRNA (miRNA) sequences search against whole genome (chromosome) prediction of likely PCR products and search for potential mismatches of the specified primers or probes. Search for multiple targets simultaneously within a specified range. In silico PCR primer searching is useful for the discovery of melting temperature target-binding sites.

PCR, Multiplex, and QF-PCR primer design & genotyping tool

This application offers advanced capabilities for designing primers across a wide range of PCR applications, including standard, inverse, multiplex, quantitative fluorescence (TaqMan and MGB-probe assay design), and bisulfite PCR. It also supports the development and validation of primer sets for genotyping single nucleotide polymorphisms (SNP) and insertions/deletions (InDel). Additionally, all individual tasks can be efficiently multiplexed for high-throughput analysis, such as fluorescence probe-based multiplex real-time qPCR assays.

KASP primers genotyping assay design tool

Allele-Specific PCR (AS-PCR) - KASPâ„¢ (Kompetitive Allele Specific PCR) or PACEâ„¢ (PCR Allele Competitive Extension) or Allele-Specific Quantitative PCR (ASQ) - based genotyping assay designs for multiallelic discrimination of single nucleotide polymorphisms (SNPs) and insertions and deletions (InDels) at specific loci. The application for genotyping assay design for SNP/InDel-specific KASP assay-targeting primers (KASP Assay Mix).

Loop-mediated Isothermal Amplification (LAMP) primer design tool

Loop-mediated Isothermal Amplification (LAMP) uses 4-6 primers recognizing 6-8 distinct regions of target DNA for a highly specific amplification reaction. LAMP is a highly sensitive, specific, and rapid DNA amplification technique that has revolutionized molecular biology research and clinical diagnostics. LAMP reactions occur under isothermal conditions, and do not require special thermal cyclers. The LAMP assay can also be used for bisulfite LAMP primer design.

Gibson assembly primer design tool

Gibson Cloning is a technique for assembling DNA constructs that allows multiple linear segments to be joined either into a single large linear segment or, if the segments contain the appropriate components and overlap, into an intact plasmid. An isothermal, single-reaction method for the assembly of multiple overlapping DNA molecules by the concerted action of a 5′ exonuclease, a DNA polymerase and a DNA ligase. This assembly method can be used to seamlessly construct synthetic and natural genes, genetic pathways and entire genomes, and could be a useful molecular engineering tool.

PrimerAnalyser

It provides a comprehensive analysis of sequences with both standard and mixed bases. The tool calculates the physical properties of the sequence, including the length, GC content, melting temperature, molecular weight, extinction coefficient, optical density (OD), sequence linguistic complexity, and self-dimer detection. The melting temperature calculations were based on nearest-neighbor thermodynamic parameters for standard and mixed oligonucleotides, including LNA modifications. It also provides a dilution and resuspension calculator for the stocks.

PrimersList

Analyzes different features of multiple primers simultaneously, including the melting temperature calculation for standard and mixed oligonucleotides, GC content, sequence linguistic complexity, molecular weight, the extinction coefficient, and the optical density (OD); primers are analyzed for all secondary structures, including self-dimers and cross-dimers in primer pairs.

PCR reaction setup calculator

PCR, Loop-mediated Isothermal Amplification (LAMP) or any reaction setup calculator.

Universal dilution and mixing two solutions calculator

A dilution calculator is applicable for mixing two solutions with various concentrations (molar, %, or other), different pH levels, or mixing the stock solution with a solvent like water.

Oligo probe design for the Gator GeneSwift assay

Gator Bio’s GeneSwift Assay is a simple, fast, and reliable method for determining the titer. It streamlines a two-step procedure involving AAV lysis and genome hybridization within a single tube, which is succeeded by biolayer interferometry detection.