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


IUPAC DNA degenerate code is an extended vocabulary of 11 letters which allows the description of ambiguous DNA code. Each letter represents a combination of one or several nucleotides:
B=(C,G,T), D=(A,G,T), H=(A,C,T), K=(G,T), M=(A,C), N=(A,C,G,T), R=(A,G), S=(G,C), V=(A,C,G), W=(A,T), Y=(C,T).
U=Uracil; I=Inosine; and LNA: dA=E, dC=F, dG=J, dT=L.

Guedin A, Gros J, Alberti P, Mergny J. 2010. How long is too long? Effects of loop size on G-quadruplex stability. Nucleic Acids Res, 38(21):7858-7868.

Watkins NE, SantaLucia JJ 2005. Nearest-neighbor thermodynamics of deoxyinosine pairs in DNA duplexes. Nucleic Acids Res, 33(19): 6258-6267.

McTigue, Patricia M, Peterson, Raymond J, and Kahn, Jason D 2004. Sequence-dependent thermodynamic parameters for Locked Nucleic Acid (LNA)-DNA duplex formation. Biochemistry, 43:5388-5405.

SantaLucia J 1998. A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics. PNAS, 95:1460-1465.

Xia T, SantaLucia J Jr, Burkard ME, Kierzek R, Schroeder SJ, Jiao X, Cox C, Turner DH 1998. Thermodynamic parameters for an expanded nearest-neighbor model for formation of RNA duplexes with Watson-Crick base pairs. Biochemistry, 37(42):14719-35.



The tools are written in Java with NetBeans IDE (Apache) and require the Java 8 Runtime Environment (Java SE 8 Platform) or use OpenWebStart an open source reimplementation of the Java Web Start technology for latest Java SE 17 (LTS) or Java SE 19.

Understanding a Java error message:
If the Java security level is set to "Very High" then no unsigned Java programs are allowed to execute.

Solution:
Add http://primerdigital.com/ site to "Exception Site List", and set "Security Level" to High.
Download a Certificate file, import it to "Signer CA" at Java Control Panel:
Java Control Panel

Contact
Dr. Ruslan Kalendar


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



Copyright

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These computer programs are protected by copyright law and international treaties.
Unauthorized reproduction or distribution of this program, or any portion of it, maybe result in severe civil and criminal penalties and will be prosecuted to the maximum extent possible under the 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 this software with the purpose is to "transcoding" or converting application content into alternate programs.