References
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]
- Allawi HT, SantaLucia J 1997. Thermodynamics and NMR of internal G-T mismatches in DNA. Biochemistry, 36:10581-10594
- Allawi HT, SantaLucia JJr 1998. NMR solution structure of a DNA dodecamer containing single G*T mismatches. Nucleic Acids Res, 26(21):4925-34
- Bommarito S, Peyret N, SantaLucia J 2000. Thermodynamic parameters for DNA sequences with dangling ends. Nucleic Acids Res, 28:1929-1934
- 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
- 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
- Freier SM, Kierzek R, Jaeger JA, Sugimoto N, Caruthers MH, Neilson T, Turner DH 1986. Biochemistry, 83:9373-9377
- Gabrielian A, Bolshoy A 1999. Sequence complexity and DNA curvature. Computer & Chemistry, 23:263-274.
- Gadberry Michael D, Malcomber Simon T, Doust Andrew N, Kellogg Elizabeth A 2005. Primaclade—a flexible tool to find conserved PCR primers across multiple species. Bioinformatics, 21(7): 1263-1264.
- 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.
- Jakob Fredslund, Mette Lange 2007. Primique: automatic design of specific PCR primers for each sequence in a family. BMC Bioinformatics, 8:369
- 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.
- Kalendar R, GrobT, Regina M, Suoniemi A, Schulman AH 1999. IRAP and REMAP: Two new retrotransposon-based DNA fingerprinting techniques. Theoretical and Applied Genetics, 98: 704-711.
- Kalendar R, Schulman AH 2006. IRAP and REMAP for retrotransposon-based genotyping and fingerprinting. Nature Protocols, 1(5):2478-2484.
- 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 Res, 29(22):4633-42. Kurtz S: The VMATCH large scale sequence analysis software. [http://www.vmatch.de]
- Le Novcre 2001. MELTING, a free tool to compute the melting temperature of nucleic acid duplex. Bioinformatics, 17:1226-1227.
- Lefebvre A, Lecroq T, Dauchel H, Alexandre J. FORRepeats: detects repeats on entire chromosomes and between genomes. Bioinformatics. 2003, 19(3):319-26.
- Lexa M, Horak J, Brzobohaty B 2001. Virtual PCR. Bioinformatics, 17(2):192-193. Lexa M, Valle G 2003. PRIMEX: rapid identification of oligonucleotide matches in whole genomes. Bioinformatics, 19(18):2486-2488.
- Lowe T., Sharefkin J., Yang S.Q., Dieffendach C.W. 1990. A computer program for selection of oligonucleotide primers for PCR. Nucleic Acids Res, 18: 1757-1562.
- McCarthy EM, McDonald JF 2003. LTR_STRUC: a novel search and identification program for LTR retrotransposons. Bioinformatics, 19(3):362-367.
- Morgenstern B. 1999. DIALIGN 2: improvement of the segment-to-segment approach to multiple sequence alignment. Bioinformatics, 15:211-218.
- 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. Nucl Acids Res. 30: e37
- Nicolas von Ahsen, Carl T. Wittwer, Ekkehard Schutz 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.
- 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 Res, 28(9):1879-1884.
- Novere Le 2001. MELTING, a free tool to compute the melting temperature of nucleic acid duplex. Bioinformatics, 17, 1226-1227.
- Orlov YL, Potapov VN 2004. Complexity: an internet resource for analysis of DNA sequence complexity. Nucleic Acids Res, 32: W628-W633.
- 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
- Peyret N, Seneviratne PA, Allawi HT, SantaLucia J. Jr. 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.
- Rho M, Choi JH, Kim S, Lynch M, Tang H 2004. De novo identification of LTR retrotransposons in eukaryotic genomes. BMC Genomics, 8:90.
- Rubin E, Levy AA 1996.A mathematical model and a computerized simulation of PCR using complex templates. Nucleic Acids Res, 24(18):3538-3545.
- Rychlik W, Spencer WJ, Rhoads RE 1990. Optimization of the annealing temperature for DNA amplification in vitro. Nucleic Acids Res, 11; 18(21): 6409-6412.
- Bommarito N, Peyret JS Jr 2000. Thermodynamic parameters for DNA sequences with dangling ends. Nucleic Acids Res, 28(9): 1929-1934.
- SantaLucia JJr, 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.
- SantaLucia JJr, Hicks D 2004. The thermodynamics of DNA structural motifs. Annu. Rev. Biophys. Biomol. Struct., 33, 415-40.
- Steve Rozen, Helen J Skaletsky 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
- 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.
- 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
- Sugimoto N, Nakano S, Yoneyama M, Honda K 1996. Improved thermodynamic parameters and helix initiation factor to predict stability of DNA duplexes. Nucleic Acids Res, 24: 4501-4505
- 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 Res, 23(21), 4407-14.
- Waugh R, McLean K, Flavell AJ, Pearce SR, Kumar A, Thomas BB, Powell W. 1997. Genetic distribution of Bare-1-like retrotransposable elements in the barley genome revealed by sequence-specific amplification polymorphisms (S-SAP). Mol Gen Genet. 253(6), 687-94.
- Welsh J, McClelland M Fingerprinting genomes using PCR with arbitrary primers. 1990. Nucleic Acids Res, 18, 7213-7218.
- Wetmur JG 1991. DNA probes: applications of the principles of nucleic acid hybridization. Crit Rev Biochem Mol Biol, 26: 227-259.
- Williams JGK, Kubelik AR, Livak KL, Rafalscki JA, Tingly SV 1990. DNA polymorphisms amplified by arbitrary primers are useful as genetic markers. Nucleic Acids Res, 18, 6513-6535.
- 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
- Xiaohan Yang, Brian E Scheffler and Leslie A Weston 2006. Recent developments in primer design for DNA polymorphism and mRNA profiling in higher plants. Plant Methods, 2:4 doi:10.1186/1746-4811-2-4
- Xu Z, Wang H 2007. LTR_FINDER: an efficient tool for the prediction of full-length LTR retrotransposons. Nucleic Acids Res, 35(Web Server issue):W265-8.
- Zietkiewicz E, Rafalski A, Labuda D. 1994. Genome fingerprinting by simple sequence repeat (SSR)-anchored polymerase chain reaction amplification. Genomics, 20, 176-183.