Efficient identification of DNA hybridization partners in a sequence database

Bioinformatics

Volumn 22, Issue 14, 2006, Pages

  Mann, Tobias P ^a   Noble, William Stafford ^a,b  

^a UNIVERSITY OF WASHINGTON   (United States)

^b University of Washington   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEMENTARY DNA; GENOMIC DNA;

ACCURACY; BINDING SITE; CONFERENCE PAPER; DNA BINDING; DNA HYBRIDIZATION; DNA SEQUENCE; GENETIC ALGORITHM; HUMAN; HUMAN GENOME; MICROARRAY ANALYSIS; OLIGONUCLEOTIDE PROBE; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; SEQUENCE DATABASE;

EID: 33747892658     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/btl240     Document Type: Conference Paper

References (24)

1. S. F. Altschul, W. Gish, W. Miller, E. W. Myers, and D. J. Lipman. A basic local alignment search tool. 215: 403-410, 1990.
2. A. Andersson, R. Bernander, and P. Nilsson. Dual-genome primer design for construction of DNA microarrays. Bioinformatics, 21(3): 325-332, 2005.
3. Q. Chou, M. Russell, D. E. Birch, J. Raymond, and W. Bloch. Prevention of pre-PCR mis-priming and primer dimerization improves low-copy-number amplifications. 20(7):1717 -1723, 1992.
4. R. A. Dimitrov and M. Zuker. Prediction of hybridization and melting for double stranded nucleic acids. Biophys. Journal, 87(1): 215-226,2004.
5. ENCODE Project Consortium. The ENCODE (ENcyclopedia of DNA Elements) project. Science, 306: 636-640, 2004.
6. T. Garel and H. Orland. Generalized Poland-Scheraga model for DNA hybridization. Biopolymers, 75(6): 453-467, 2004.
7. D. Gusfield. Algorithms on Strings, Trees, and Sequences. Cambridge University Press, Cambridge, UK, 1997.
8. S. A. Haas, M. Hild, A. P. H. Wright, T. Hain, D. Talibi, and M. Vingron. Genome-scale design of PCR primers and long oligomers for DNA microarrays. Nucleic Acids Res., 31(19): 5576-5581, 2003.
9. M. A. Innis, D. H. Gelfand, and J. J. Sninsky. PCR Applications: Protocols for Functional Genomics. Academic Press, 1999.
10. B. Kaltenboeck and C.M. Wang. Advances in real-time PCR: Application to clinical laboratory diagnostics. Adv. in Clin. Chem., 40:219-259, 2005.
11. W.J. Kent, C. W. Sugnet, T.S. Furey, K.M. Roskin, T.H. Pringle, A.M. Zahler, and D. Haussler. The human genome browser at UCSC. Genome Res., 12(6): 996-1006, 2002.
12. T. Lowe, J. Sharefkin, S. Q. Yang, and C. W. Dieffenbach. A computer program for selection of oligonucleotide primers for polymerase chain reactions. Nucleic Acids Res., 18(7):1757 -1761, 1990.
13. U. Manber and E. Myers. Suffix arrays:a new method for on-line search. SIAM J. Comput., 2: 935-948, 1993.
14. N. Markham and M. Zuker. DINAMelt web server for nucleic acid melting prediction. Nucleic Acid Res., 33: W577-W581, 2004.
15. D. H. Mathews, J. Sabina, M. Zuker, and D. H. Turner. Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure. J. Mol. Biol., 288: 911-940, 1999.
16. R. K. Saiki, D. H. Gelfand, S. Stoffel, S.J. Scharf, R. Higuchi, G. T. Horn, K. B. Mullis, and H.A.Erlich. Primer-directed enzymatic amplification of DNA with a thermostable polymerase. Science, 239(4839): 487-491, 1988.
17. J. SantaLucia, Jr. A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics. Proc. Natl Acad. Sci. USA, 95: 1460-1465, 1998.
18. J. SantaLucia, Jr and D. Hicks. The thermodynamics of DNA structural motifs. Annu. Rev. Biophys. Biomol. Struct., 33: 415-440, 2004.
19. M. Schena, D. Shalon, R. W. Davis, and P. O. Brown. Quantitative monitoring of gene expression patterns with a complementary DNA microarray. 270: 467-470, 1995.
20. R. B. Stoughton. Applications of DNA microarrays in biology. Annual Rev. Biochem., 74: 53-82, 2005.
21. X. Wang and B. Seed. A PCR primer bank for quantitative gene expression analysis. Nucleic Acids Res., 31(24): E154, 2003.
22. M.L. Wong and J.F. Medrano. Real-time PCR for mRNA quantitation. Biotech., 39: 75-85, 2005.
23. W. Xu, W. J. Briggs, J. Padolina, W. Liu, C. R. Linder, and D. P. Miranker. Using MoBioS' scalable genome join to find conserved primer pair candidates between two genomes. Bioinformatics, 20: I355-i362, 2004.
24. N. Ben Zakour, M. Gautier, R. Andonov, D. Lavenier, P. Veber M-F. Cochet, A. Sorokin, and Y. Le Loir. GenoFrag: Software to design primers optimized for whole genome scanning by long-range PCR amplification. Nucleic Acids Res., 32(1): 17-24, 2004.