New, improved, and practical k-stem sequence similarity measures for probe design

Journal of Computational Biology

Volumn 15, Issue 5, 2008, Pages 525-534

  Macula, Anthony J ^a   Schliep, Alexander ^b   Bishop, Morgan A ^a   Renz, Thomas E ^c  

^a STATE UNIVERSITY OF NEW YORK   (United States)

^b MAX PLANCK INSTITUTE FOR MOLECULAR GENETICS   (Germany)

^c AIR FORCE RESEARCH LABORATORY   (United States)

Author keywords

Bit vector; BLAST; Edit; Hamming; Insertion deletion; Nearest neighbor; Probe; Sequence similarity; Target

Indexed keywords

NUCLEOTIDE; OLIGONUCLEOTIDE; SINGLE STRANDED DNA;

ALGORITHM; ARTICLE; COMPUTER PROGRAM; GENE DELETION; GENE INSERTION; MOLECULAR PROBE; PRIORITY JOURNAL; PROTEIN MOTIF; THERMODYNAMICS; BASE PAIRING; CHEMISTRY; CONFORMATION; METHODOLOGY; NUCLEOTIDE SEQUENCE; OLIGONUCLEOTIDE PROBE; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS;

ALGORITHMS; BASE PAIRING; BASE SEQUENCE; DNA, SINGLE-STRANDED; NUCLEIC ACID CONFORMATION; OLIGONUCLEOTIDE PROBES; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, PROTEIN;

EID: 53049101939     PISSN: 10665277     EISSN: None     Source Type: Journal    
DOI: 10.1089/cmb.2007.0208     Document Type: Article

References (26)

1. Allison, L., and Dix, T.L. 1986. A bit-string longest common subsequence algorithm. Inform. Process. Lett. 23, 305-310.
2. Andronescu, M., Aguirre-Hernandez, R., Condon, A., et al. 2003. RNAsoft: a suite of RNA secondary structure prediction and design software tools. Nucleic Acids Res. 31, 3416-3422.
3. Cai, H., White, P., Torney, D., et al. 2000. Flow cytometry-based minisequencing: a new platform for high throughput single nucleotide polymorphism scoring. Genomics 66, 135-143.
4. Crochemore, M., Iliopoulos, C.S., Pinzon, Y.J., et al. 2001. A fast and practical bit-vector algorithm for the longest common subsequence problem. Inform. Process. Lett. 80, 279-285.
5. D'yachkov, A., Macula, A., Pogozelski, W., et al. 2005a. A weighted insertion deletion stacked pair thermodynamic metric for DNA codes. Lect. Notes Comput. Sci. 3384, 90-103.
6. Dyachkov, A., Macula, A., Pogozelski, W., et al. 2006. New t-gap insertion-deletion like metrics for DNA hybridization thermodynamic modeling. J. Comput. Biol. 13, 866-881.
7. D'yachkov, A., Vilenkin, P., Ismagilov, I., et al. 2005b. On DNA codes. Problems Inform. Transm. 41, 349-367.
8. Fish, D.J., Horne, M.T., and Brewood, G.P. 2007. DNA multiplex hybridization on microarrays and thermodynamic stability in solution: a direct comparison. Nucleic Acids Res. 35, 7197-7208.
9. Gusfield, D. 1997. Algorithms on Strings, Trees, and Sequences: Computer Science and Computational Biology. Cambridge University Press, Cambridge.
10. Hyyrö, H., Pinzon, Y., and Shinohara, A. 2005. New bit-parallel indel-distance algorithm. Lect. Notes Comput. Sci. 3503, 380-390.
11. Kaderali, L., Deshpande, A., Nolan, J., et al. 2003. Primer-design for multiplexed genotyping. Nucleic Acids Res. 31, 1796-1802.
12. Kane, M.D., Jatkoe, T.A., Stumpf, C.R., et al., 2000. Assessment of the specificity and sensitivity of oligonucleotide (50mer) microarrays. Nucleic Acid Res. 28, 4552-4557.
13. Karaman, M.W., Groshen, S., Lee, C., et al. 2005. Comparisons of substitution, insertion and deletion probes for resequencing and mutational analysis using oligonucleotide microarrays. Nucleic Acids Res. 33, e33.
14. Li, F., and Stormo, G. 2001. Selection of optimal DNA oligos for gene expression arrays. Bioinformatics 17, 1067-1076.
15. Li, X., He, Z., and Zhou, J. 2005. Selection of optimal oligonucleotide probes for microarrays using multiple criteria, global alignment and parameter estimation. Nucleic Acids Res. 33, 6114-6123.
16. Mathews, D., Zuker, M., and Turner, D. 2006. RNAstructure 4.2. Available at http://rna.chem.rochester.edu. Accessed May 10, 2008.
17. Myers, E.W. 1999. A fast bit-vector algorithm for approximate stringmatching based on dynamic programming. J. ACM 46, 539-553.
18. Nordberg, E.K. 2005. YODA: selecting signature oligonucleotides. Bioinformatics 21, 1365-1370.
19. Pozhitkov, A., Noble, P.A., Domazet-Los, T., et al. 2006. Tests of rRNA hybridization to microarrays suggest that hybridization characteristics of oligonucleotide probes for species discrimination cannot be predicted. Nucleic Acids Res. 34, e66.
20. Pozhitkov, A.E., Tautz, D., and Noble, P.A. 2007. Oligonucleotide microarrays: widely applied: poorly understood. Brie. Funct. Genom. Proteom. 6, 141-148.
21. SantaLucia, J. 1998. A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics, Proc. Natl. Acad. Sci. USA 95, 1460-1465.
22. SantaLucia, J., and Hicks, D. 2004. The thermodynamics of DNA structural motifs. Annu. Rev. Biophys. Biomol. Struct. 33, 415-440.
23. Schliep, A., Torney, D.C., and Rahmann, S. 2003. Group testing with DNA chips: generating designs and decoding experiments. Proc. IEEE Comput. Soc. Conf. Bioinform. 84-91.
24. Wu, C.T., Liao, C.Y., and Su, H.J. 2003. IMPORT-integrated massive probe's optimal recognition tools. Genome Inform. 14, 478-479.
25. Zhang, L., Wu, C., Carta, R., et al. 2007. Free energy of DNA duplex formation on short oligonucleotide microarrays. Nucleic Acids Res. 35, e18.
26. Zuker, M., Mathews, D., and Turner, D. 1999. Algorithms and thermodynamics for RNA secondary structure prediction: a practical guide. In: Barciszewski, J., and Clark, B.F.C., eds., RNA Biochemistry and Biotechnology. Kluwer Academic Publishers, Amsterdam, pgs. 11-45.