Webtools for PCR, qPCR, in silico PCR and oligonucleotides


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

PCR tool provides comprehensive and professional facilities for designing primers for most PCR applications and their combinations: standard, multiplex, long distance, inverse, real-time, group-specific (universal primers for phylogenetically related DNA sequences) and unique (specific primers for each from phylogenetically related DNA sequences), bisulphite modification assays, polymerase extension PCR multi-fragments assembly cloning (OE-PCR); and microarray design;
in silico (virtual) PCR or primers and probes search or in silico PCR against whole genome(s) or a list of chromosome - prediction of probable PCR products and search of potential mismatching location of the specified primers or probes;
comprehensive primer test, the melting temperature calculation for standard and degenerate oligonucleotides including LNA and other modifications, primer PCR efficiency, primer's linguistic complexity, and dilution and resuspension calculator;
analyzes different features of multiple primers simultaneously, the melting temperature, GC content, sequence linguistic complexity, primer PCR efficiency and molecular weight, the extiction coefficient, the optical density (OD);
primers (probes) are analyzed for all primer secondary structures including the alternative hydrogen bonding to Watson-Crick base pairing such as G-quadruplexes or wobble base pairs (like G-G, G-T, G-A), hairpins, self-dimers and cross-dimers in primer pairs;
tool calculate Tm for primer dimers with mismatches for pure and mixed bases using averaged nearest neighbour thermodynamic parameters and for modifications (inosine, uridine, or LNA);
tool for identifying simple sequence repeat (SSR) loci by analysing the low complexity regions of input sequences;
tool for restriction I-II-III types enzymes and homing endonucleases analysis, find or create restriction enzyme recognition sites for coding sequences;
tool for searching for similar sequences (or primers);
translates nucleotide (DNA/RNA) sequences to the corresponding peptide sequence in all six frames for standard and degenerate DNA and modifications (inosine, uridine);
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;
the program includes various bioinformatics tools for patterns analysis of sequences with GC:(G-C)/(G+C), AT:(A-T)/(A+T), SW:(S-W)/(S+W), MK:(M-K)/(M+K), purine-pyrimidine (R-Y)/(R+Y) skews, CG% content and the melting temperature and considers linguistic sequence complexity profiles.

jPCR Web Start or


PrimerAnalyser

provides comprehensive analysis of sequence with standard and mixed bases, as well as DNA, RNA, methylated, locked and phosphorothioated bases; tool will calculate the physical properties of the sequence including length, CG content, melting temperature, molecular weight, the extiction coefficient, the optical density (OD), sequence linguistic complexity, primer PCR efficiency, self-dimers and G-quadruplexes detection.
The melting temperature calculations are based on nearest neighbour thermodynamic parameters for standard and degenerate oligonucleotides including LNA and other modifications. And provides a dilution and resuspension calculator for stocks.

PrimerAnalyser Web Start or


PrimersList

Analyzes different features of multiple primers simultaneously, the melting temperature calculation for standard and degenerate oligonucleotides, GC content, primer PCR efficiency, sequence linguistic complexity, molecular weight, the extiction coefficient, the optical density (OD);
primers are analyzed for all primer secondary structures including G-quadruplexes detection, hairpins, self-dimers and cross-dimers in primer pairs;
the optimal temperature of annealing (Ta) calculation for all given primers.

PrimersList Web Start or


PCR reaction setup calculators

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

PCR reaction setup calculators Web Start or


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.



Comparison of primer design and oligonucleotide analysing tools versus other most popular on-line primer design and analysing packages.




The tools are written in Java with NetBeans IDE (Oracle) and require the Java Runtime Environment (JRE) on a computer.

Note: If you don't see the Java Web Start application's Java Web Start button, Java application needs the Java Runtime Environment (JRE) or complete Java Development Kit (JDK), can be downloaded from java.com), and you might need to enable the JavaScript interpreter in your browser so that the Deployment Toolkit script can function properly.

To determine which version of Java your web browser is using, please visit javatester or java.com.

UNDERSTANDING A JAVA ERROR MESSAGE:
If the Java 7 security level is set to "Very High" then no unsigned Java programs are allowed to execute. The error message is "Application Blocked by Security Settings ... Your security settings have blocked an untrusted application from running". The message refers to an "untrusted" application when it really is describing an unsigned application.
Solution:
set "Security Level" to Medium (Least secure setting - All Java applications will be allowed to run after presenting a security prompt.)

Java Web Start

Contact
Dr. Ruslan Kalendar


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

Kalendar R, Lee D, Schulman AH 2011. Java web tools for PCR, in silico PCR, and oligonucleotide assembly and analysis. Genomics, 98(2): 137-144. DOI: 10.1016/j.ygeno.2011.04.009

Kalendar R, Lee D, Schulman AH 2014. FastPCR software for PCR, in silico PCR, and oligonucleotide assembly and analysis. DNA Cloning and Assembly Methods, Methods in Molecular Biology, Svein Valla and Rahmi Lale (ed.), Humana Press, 1116: 271-302; ISBN 978-1-62703-763-1, DOI: 10.1007/978-1-62703-764-8_18

Copyright

The copyrights and other rights to the materials on the PrimerDigital website are owned by PrimerDigital.
These computer programs are protected by copyright law and international treaties.
Unauthorized reproduction or distribution of this program, or any portion of it, may be result in severe civil and criminal penalties, and will be prosecuted to the maximum extent possible under law.
You are also expressly prohibited from reverse engineering, decompiling, translating, disassembling, deciphering, decrypting, or otherwise attempting to discover the source code of the licensed works as the licensed works contain proprietary material of licensor.
You are prohibited from using these software with a commercial software or hardware product ("commercial product") whose purpose is to "transcode" or convert application content into an alternate programs.