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.
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.
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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, 1116: 271-302. DOI: 10.1007/978-1-62703-764-8_18
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
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