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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 (Oracle) and require the Java 8 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 8 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.

UNDERSTANDING A JAVA ERROR MESSAGE:
If the Java 8 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:

Kalendar R, Khassenov B, Ramankulov Y, Samuilova O, Ivanov KI 2017. FastPCR: an in silico tool for fast primer and probe design and advanced sequence analysis. Genomics, 109: 312-319. DOI:10.1016/j.ygeno.2017.05.005

Kalendar R, Muterko A, Shamekova M, Zhambakin K 2017. In silico PCR tools a fast primer, probe and advanced searching. Methods in Molecular Biology, 1620: 1-31. DOI:10.1007/978-1-4939-7060-5_1

Kalendar R, Tselykh T, Khassenov B, Ramanculov EM 2017. Introduction on using the FastPCR software and the related Java web tools for PCR, in silico PCR, and oligonucleotide assembly and analysis. Methods in Molecular Biology, 1620: 33-64. DOI:10.1007/978-1-4939-7060-5_2

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