PrimerDigital

Reference apply to all FasPCR update, if you use FastPCR in your work please cite:

Kalendar R, Lee D, Schulman AH 2009. FastPCR Software for PCR Primer and Probe Design and Repeat Search. Genes, Genomes and Genomics, 3(1):1-14. [http://primerdigital.com/fastpcr.html]

• 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.
• Guédin A, Gros J, Alberti P, Mergny J 2010. How long is too long? Effects of loop size on G-quadruplex stability. Nucleic Acids Research, 38(21):7858-7868. (See more about the quadruplex here: Quadruplex.org)
• Owczarzy R, Tataurov AV, Wu Y, Manthey JA, McQuisten KA, Almabrazi HG, Pedersen KF, Lin Y, Garretson J, McEntaggart NO, Sailor CA, Dawson RB, Peek AS 2008. IDT SciTools: a suite for analysis and design of nucleic acid oligomers. Nucleic Acids Research, 1:W163-169
• Rachwal PA, Fox KR 2007. Quadruplex melting. Methods, 43:291-301.
• Fredslund J, Lange M 2007. Primique: automatic design of specific PCR primers for each sequence in a family. BMC Bioinformatics, 8:369
• Xu Z, Wang H 2007. LTR_FINDER: an efficient tool for the prediction of full-length LTR retrotransposons. Nucleic Acids Research, 35:W265-8.
• Burge S, Parkinson GN, Hazel P, Todd AK, Neidle K 2006. Quadruplex DNA: sequence, topology and structure. Nucleic Acids Research, 34:5402-5415.
• Yang X, Scheffler BE, Weston LA 2006. Recent developments in primer design for DNA polymorphism and mRNA profiling in higher plants. Plant Methods, 2:4.
• Watkins NE, SantaLucia JJ 2005. Nearest-neighbor thermodynamics of deoxyinosine pairs in DNA duplexes. Nucleic Acids Research, 33(19):6258-6267.
• Gadberry MD, Malcomber ST, Doust AN, Kellogg EA 2005. Primaclade - a flexible tool to find conserved PCR primers across multiple species. Bioinformatics, 21(7):1263-1264.
• Jurka J, Kapitonov VV, Pavlicek A, Klonowski P, Kohany O, Walichiewicz J 2005. Repbase Update, a database of eukaryotic repetitive elements. Cytogenetic and Genome Research, 110:462-467.
• Orlov YL, Potapov VN 2004. Complexity: an internet resource for analysis of DNA sequence complexity. Nucleic Acids Research, 32:W628-W633.
• Rho M, Choi JH, Kim S, Lynch M, Tang H 2004. De novo identification of LTR retrotransposons in eukaryotic genomes. BMC Genomics, 8:90.
• SantaLucia JJ, Hicks D 2004. The thermodynamics of DNA structural motifs. Annu. Rev. Biophys. Biomol. Struct, 33:415-40.
• Lefebvre A, Lecroq T, Dauchel H, Alexandre J 2003. FORRepeats: detects repeats on entire chromosomes and between genomes. Bioinformatics, 19(3):319-26.
• Lexa M, Valle G 2003. PRIMEX: rapid identification of oligonucleotide matches in whole genomes. Bioinformatics, 19(18):2486-2488.
• McCarthy EM, McDonald JF 2003. LTR_STRUC: a novel search and identification program for LTR retrotransposons. Bioinformatics, 19(3):362-367.
• Nazarenko I, Lowe B, Darfler M, Ikonomi P, Schuster D, Rashtchian A 2002. Multiplex quantitative PCR using self-quenched primers labeled with a single fluorophore. Nucleic Acids Research, 30:e37
• Lexa M, Horak J, Brzobohaty B 2001. Virtual PCR. Bioinformatics, 17(2):192-193.
• Chou SH, Chin KH 2001. Solution structure of a DNA double helix incorporating four consecutive non-Watson-Crick base-pairs. J Mol Biol, 312(4):769-81.
• Fiandaca MJ, Hyldig-Nielsen JJ, Gildea BD, Coull JM 2001. Self-Reporting PNA/DNA Primers for PCR Analysis. Genome Research, 11(4):609-613.
• Kurtz S, Choudhuri JV, Ohlebusch E, Schleiermacher C, Stoye J, Giegerich R 2001. REPuter: the manifold applications of repeat analysis on a genomic scale. Nucleic Acids Research, 29(22):4633-42.
• Kurtz S: The VMATCH large scale sequence analysis software.
• Le Novcre 2001. MELTING, a free tool to compute the melting temperature of nucleic acid duplex. Bioinformatics, 17:1226-1227.
• Ahsen N, Wittwer CT, Schutz E 2001. Oligonucleotide Melting Temperatures under PCR Conditions: Nearest-Neighbor Corrections for Mg²⁺, Deoxynucleotide Triphosphate, and Dimethyl Sulfoxide Concentrations with Comparison to Alternative Empirical Formulas. Clin Chem, 47:1956-1961.
• Bommarito S, Peyret N, SantaLucia J 2000. Thermodynamic parameters for DNA sequences with dangling ends. Nucleic Acids Research, 28:1929-1934.
• Nishigaki K, Saito A, Takashi H, Naimuddin M 2000. Whole genome sequence-enabled prediction of sequences performed for random PCR products of Escherichia coli. Nucleic Acids Research, 28(9):1879-1884.
• Bommarito N, Peyret JS Jr 2000. Thermodynamic parameters for DNA sequences with dangling ends. Nucleic Acids Research, 28(9):1929-1934.
• Rozen S, Skaletsky HJ 2000. Primer3 on the WWW for general users and for biologist programmers. In: Krawetz S, Misener S (eds) Bioinformatics Methods and Protocols: Methods in Molecular Biology. Humana Press, Totowa, NJ, pp 365-386.
• Kalendar R, Grob T, Regina M, Suoniemi A, Schulman AH 1999. IRAP and REMAP: Two new retrotransposon-based DNA fingerprinting techniques. Theoretical and Applied Genetics, 98:704-711.
• Gabrielian A, Bolshoy A 1999. Sequence complexity and DNA curvature. Computer & Chemistry, 23:263-274.
• Morgenstern B 1999. DIALIGN 2: improvement of the segment-to-segment approach to multiple sequence alignment. Bioinformatics, 15:211-218.
• Peyret N, Seneviratne PA, Allawi HT, SantaLucia JJ 1999. Nearest-neighbor thermodynamics and NMR of DNA sequences with internal A.A, C.C, G.G, and T.T mismatches. Biochemistry, 38:3468-3477.
• Allawi HT, SantaLucia JJ. 1998. NMR solution structure of a DNA dodecamer containing single G*T mismatches. Nucleic Acids Research, 26(21):4925-34.
• Xia T, SantaLucia J, Burkard ME, Kierzek R, Schroeder SJ, Jiao X, Cox C, Turner DH. 1998. Thermodynamics parameters for an expanded nearest-neighbor model for formation of RNA duplexes with Watson-Crick base pairs. Biochemistry, 37:14719-14735
• Allawi HT, SantaLucia JJ. 1997. Thermodynamics and NMR of internal G-T mismatches in DNA. Biochemistry, 36:10581-10594.
• Gilson MK, Given JA, Bush BL, McCammon JA 1997. The statistical-thermodynamic basis for computation of binding affinities: a critical review. Biophys J, 72(3):1047-1069.
• Rubin E, Levy AA. 1996. A mathematical model and a computerized simulation of PCR using complex templates. Nucleic Acids Research, 24(18):3538-3545.
• SantaLucia JJ, Allawi HT, Seneviratne PA 1996. Improved nearest-neighbor parameters for predicting DNA duplex stability. Biochemistry, 35:3555-3562.
• SantaLucia JJ 1998. A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbour thermodynamics. Proc. Natl. Acad. Sci. USA, 95:1460-1465.
• Sugimoto N, Nakano S, Yoneyama M, Honda K 1996. Improved thermodynamic parameters and helix initiation factor to predict stability of DNA duplexes. Nucleic Acids Research, 24:4501-4505.
• Sugimoto N, Nakano S, Katoh M, Matsumura A, Nakamuta H, Ohmichi T, Yoneyama M, Sasaki M 1995. Thermodynamic parameters to predict stability of RNA/DNA hybrid duplexes. Biochemistry, 34:11211-11216.
• Vos P, Hogers R, Bleeker M, Reijans M, van de Lee T, Hornes M, Frijters A, Pot J, Peleman J, Kuiper M, et al. 1995. AFLP: a new technique for DNA fingerprinting. Nucleic Acids Research, 23(21):4407-14.
• Sugimoto N, Katoh M, Nakano S, Ohmichi T, Sasaki M 1994. RNA/DNA hybrid duplexes with identical nearest-neighbor base-pairs have identical stability. FEBS Letters, 354:74-78.
• Sen D, Gilbert W 1992. Guanine quartet structures. Methods Enzymol, 211:191-9.
• Wetmur JG 1991. DNA probes: applications of the principles of nucleic acid hybridization. Crit Rev Biochem Mol Biol, 26:227-259.
• Lowe T, Sharefkin J, Yang SQ, Dieffendach CW 1990. A computer program for selection of oligonucleotide primers for PCR. Nucleic Acids Research, 18:1757-1562.
• Welsh J, McClelland M 1990. Fingerprinting genomes using PCR with arbitrary primers. Nucleic Acids Research, 18:7213-7218.
• Williams JGK, Kubelik AR, Livak KL, Rafalscki JA, Tingly SV 1990. DNA polymorphisms amplified by arbitrary primers are useful as genetic markers. Nucleic Acids Research, 18:6513-6535.
• Breslauer KJ, Frank R, Blocker H, Marky LA 1986. Predicting DNA duplex stability from the base sequence. Proc. Natl. Acad. Sci. USA, 83:3746-3750.
• Freier SM, Kierzek R, Jaeger JA, Sugimoto N, Caruthers MH, Neilson T, Turner DH 1986. Improved free-energy parameters for predictions of RNA duplex stability. Biochemistry, 83:9373-9377