PrimerDigital

PrimersList

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

Write or paste your primer sequences to the input field (upper window). The analyzer accepts text and table format (can be copied from an Excel file, for example).
The name and sequence string can be separated with either space or tab, as long as the style is the same for all the primers.
The results will appear instantly in the output fields (lower windows), and update automatically if you make changes to the sequences. The results can be copied and pasted to other programs (Word, Excel, etc.).

IUPAC DNA degenerate code is an extended vocabulary of 15 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. (See more about the quadruplex here: Quadruplex.org)

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.

Note: Java application needs the Java Runtime Environment (JRE) or complete Java Development Kit (JDK) (Sun), can be downloaded from java.com), or you might need to enable the JavaScript interpreter in your browser so that the Deployment Toolkit script can function properly.

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.
[http://primerdigital.com/tools/]

Copyright

The copyrights and other rights to the materials on the PrimerDigital website are owned by PrimerDigital.
You are authorized to view the materials at this website only for your internal information purposes provided that you:
(i) retain all notices contained in the original materials;
(ii) only use images with surrounding text relating to the images; and
(iii) include the following copyright notice.
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.
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.