Webtools for PCR, qPCR, in silico PCR and oligonucleotides

PCR primer design, in silico PCR, oligonucleotide assembly and analyses

PCR tool provides comprehensive facilities for designing primers for most PCR applications and their combinations: standard, multiplex, long distance, inverse, real-time, unique, group-specific, bisulphite modification assays, polymerase extension PCR multi-fragments assembly cloning (OE-PCR);
in silico (virtual) PCR or primers and probes search, prediction of probable PCR products and search of potential mismatching location of the specified primers or probes;
analyzes different features of multiple primers simultaneously, e.g. Tm, GC content, dimer formation and else; comprehensive primer test, the melting temperature calculation for standard and degenerate oligonucleotides including LNA and other modifications, PCR efficiency, dimers detection and dilution and resuspension calculator;
analyzes different features of multiple primers simultaneously, e.g. Tm, GC content, dimer formation;
tool for identifying simple sequence repeat (SSR) loci by analysing the low complexity regions of input sequences;
Polymerase chain assembly (PCA) or oligos assembly - created to automate the design oligonucleotide sets for long sequence assembly by ligase chain reaction (LCR) and PCR.

Oligomer

Comprehensive primer test, Tm calculation, PCR efficiency, dimers detection and dilution and resuspension calculator.
Tool calculates the melting temperature for standard and degenerate oligonucleotides including LNA and other modifications. It can predict dimer formation and provides a dilution and resuspension calculator for stocks. Melting temperature calculations are based on nearest neighbour thermodynamic parameters.

PrimersList

Analyzes different features of multiple primers simultaneously, e.g. Tm, GC content, dimer formation and else; optimal Ta (temperature of annealing) calculation for all given primers.
The “PrimerList” tool provides analyses for a set of primers with prediction of oligonucleotide properties, self- and cross-dimer detection, and calculation of their melting temperatures.

PCR reaction setup calculators

PCR and qPCR reaction setup calculator; tool for planning PCR and qPCR reactions, mixing solutions.

Universal dilution and mixing two solutions calculator

Dilution calculator, applicable for mixing two solutions with various concentrations (molar or %, or other), as well as for various pH or mixing stock solution with solvent like water.

Java application needs a Java Web Start Technology (Sun) (the Java Runtime Environment (JRE) or complete Java Development Kit (JDK), for programmers only, can be downloaded from java.com).

Contact
Dr. Ruslan Kalendar

Reference apply to all Web Tools update, if you use it in your work please cite:

Kalendar R. 2010 Java web tools for PCR, in silico PCR, and oligonucleotide assembly and analyses.
[http://primerdigital.com/tools/]

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