Fast masking of repeated primer binding sites in eukaryotic genomes

Methods in Molecular Biology

Volumn 402, Issue , 2007, Pages 201-217

  Andreson, Reidar ^a   Kaplinski, Lauris ^a   Remm, Maido ^a  

^a NONE

Author keywords

DNA masking; DNA repeats; Microarrays; PCR; Primer design

Indexed keywords

EUKARYOTA;

ANIMAL; COMPUTER PROGRAM; DNA SEQUENCE; EUKARYOTIC CELL; GENOME; HUMAN; INTERNET; METHODOLOGY; NUCLEOTIDE REPEAT; POLYMERASE CHAIN REACTION; PREDICTION AND FORECASTING; REVIEW;

ANIMALS; EUKARYOTIC CELLS; GENOME; HUMANS; INTERNET; POLYMERASE CHAIN REACTION; PREDICTIVE VALUE OF TESTS; REPETITIVE SEQUENCES, NUCLEIC ACID; SEQUENCE ANALYSIS, DNA; SOFTWARE;

EID: 36048960678     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1385/1-59745-528-8:201     Document Type: Article

References (17)

1. Dawson, E., Abecasis, G.R., Bumpstead, S., Chen, Y., Hunt, S., Beare, D.M., Pabial, J., Dibling, T., Tinsley, E., Kirby, S. et al. (2002) A first-generation linkage disequilibrium map of human chromosome 22. Nature, 418, 544-548.
2. Rouchka, E.C., Khalyfa, A. and Cooper, N.G. (2005) MPrime: efficient large scale multiple primer and oligonucleotide design for customized gene microarrays. BMC Bioinformatics, 6, 175.
3. Xu, D., Li, G., Wu, L., Zhou, J. and Xu, Y. (2002) PRIMEGENS: robust and efficient design of gene-specific probes for microarray analysis. Bioinformatics, 18, 1432-1437.
4. Weckx, S., De Rijk, P., Van Broeckhoven, C and Del-Favero, J. (2005) SNPbox: a modular software package for large-scale primer design. Bioinformatics, 21, 385-387.
5. Zhang, Z., Schwartz, S., Wagner, L. and Miller, W. (2000) A greedy algorithm for aligning DNA sequences. J Comput Biol., 7, 203-214.
6. Ning, Z., Cox, A.J. and Mullikin, J.C. (2001) SSAHA: a fast search method for large DNA databases. Genome Res, 11, 1725-1729.
7. Kent, W.J. (2002) BLAT-the BLAST-like alignment tool. Genome Res, 12, 656-664.
8. Benson, G. (1999) Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res, 27, 573-580.
9. Altschul, S.F., Madden, T.L., Schaffer, A.A., Zhang, J., Zhang, Z., Miller, W. and Lipman, D.J. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res, 25, 3389-3402.
10. Rouillard, J.M., Zuker, M. and Gulari, E. (2003) OligoArray 2.0: design of oligonu-cleotide probes for DNA microarrays using a thermodynamic approach. Nucleic Acids Res, 31, 3057-3062.
11. van Hijum, S.A., de Jong, A., Buist, G., Kok, J. and Kuipers, O.P. (2003) UniFrag and GenomePrimer: selection of primers for genome-wide production of unique amplicons. Bioinformatics, 19, 1580-1582.
12. Rozen, S. and Skaletsky, H. (2000) Primer3 on the WWW for general users and for biologist programmers. Methods Mol Biol, 132, 365-386.
13. Breslauer, K.J., Frank, R., Blocker, H. and Marky, L.A. (1986) Predicting DNA duplex stability from the base sequence. Proc Natl Acad Sci USA, 83, 3746-3750.
14. SantaLucia, J., Jr. (1998) A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics. Proc Natl Acad Sci USA, 95, 1460-1465.
15. Owczarzy, R., You, Y., Moreira, B.G., Manthey, J.A., Huang, L., Behlke, M.A. and Walder, J.A. (2004) Effects of sodium ions on DNA duplex oligomers: improved predictions of melting temperatures. Biochemistry, 43, 3537-3554.
16. von Ahsen, N., Wittwer, C.T. and Schutz, E. (2001) Oligonucleotide melting temperatures under PCR conditions: nearest-neighbor corrections for Mg(2+), deoxynucleotide triphosphate, and dimethyl sulfoxide concentrations with comparison to alternative empirical formulas. Clin Chem, 47, 1956-1961.
17. Kaplinski, L., Andreson, R., Puurand, T. and Remm, M. (2005) MultiPLX: automatic grouping and evaluation of PCR primers. Bioinformatics, 21, 1701-1702.