Online tools for PCR, qPCR, LAMP, electronic PCR, analyzing primers, setting up reactions, and repeats identification

Repeats de novo identification, masking and clustering tool

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

PCR, qPCR primer design tool

The application is based on FastPCR software and provides professional facilities for designing primers for most PCR applications: standard, inverse, long-distance, real-time (TaqMan and MGB-probe assay design), and bisulfite PCR primer design.

In silico PCR tool

Virtual (in silico) or electronic PCR (ePCR) primer or probe search against whole genome(s) or a list of chromosomes - 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.

Loop-mediated Isothermal Amplification (LAMP) primer design tool

The application is based on FastPCR software and provides professional facilities for designing primers for Loop-mediated Isothermal Amplification (LAMP) applications. LAMP uses 6, including 'loop' primers recognizing 8 distinct regions of target DNA for a particular amplification reaction. The LAMP Assay can also be used for bisulfite LAMP primer design.

KASP primers 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 design for multiallelic discrimination of single nucleotide polymorphisms (SNPs) and insertions and deletions (Indels) at specific loci. The application is based on FastPCR software for genotyping assays design for SNP/InDel-specific KASP assay targeting primers (KASP Assay Mix) and the universal Master Mix.

PrimerAnalyser

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

PrimersList

Analyzes different features of multiple primers simultaneously, including the melting temperature calculation for standard and degenerate 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 and Loop-mediated Isothermal Amplification (LAMP) 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.