Optimal reconstruction of a sequence from its probes

Journal of Computational Biology

Volumn 6, Issue 3-4, 1999, Pages 361-368

  Frieze, Alan M ^a   Preparata, Franco P ^b   Upfal, Eli ^b  

^a CARNEGIE MELLON UNIVERSITY   (United States)

^b Box 1910 ^*  (United States)

Author keywords

DNA sequencing; Gapped probes; Probabilistic analysis; Sequencing by hybridization

Indexed keywords

ALGORITHM; CONFERENCE PAPER; DNA HYBRIDIZATION; DNA PROBE; DNA SEQUENCE; GENE CONSTRUCT; MATHEMATICAL MODEL; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL;

ALGORITHMS; DRUG DESIGN; EVALUATION STUDIES; MODELS, STATISTICAL; MOLECULAR PROBES; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; SEQUENCE ANALYSIS, DNA;

EID: 0032728083     PISSN: 10665277     EISSN: None     Source Type: Journal    
DOI: 10.1089/106652799318328     Document Type: Conference Paper

References (11)

1. Arratia, R., Goldstein, L., and Gordon, L. 1989. Two moments suffice for Poisson approximation: The Chen-Stein method. The Annals of Probability 17, 9-25.
2. Arratia, R., Martin, D., Reinert, G., and Waterman, M.S. 1996. Poisson process approximation for sequence repeats, and sequencing by hybridization. Journal of Computational Biology 3, 425-463.
3. Bains, W., and Smith, G.C. 1988. A novel method for DNA sequence determination. Jour. of Theoretical Biology 135, 303-307.
4. Drmanac, R., Labat, I., Bruckner, I., and Crkvenjakov, R. 1989. Sequencing of megabase plus DNA by hybridization. Genomics 4, 114-128.
5. Dyer, M.E., Frieze, A.M., and Suen, S. 1994. The probability of unique solutions of sequencing by hybridization. Journal of Computational Biology 1, 105-110.
6. Loakes, D., and Brown, D.M. 1994. 5-Nitroindole as a universal base analogue. Nucleic Acids Research 22(20), 4039-4043.
7. Lysov, Yu. P., Florentiev, V.L., Khorlin, A.A., Khrapko, K.R., Shih, V.V., and Mirzabekov, A.D. 1988. Sequencing by hybridization via oligonucleotides. A novel method. Dokl. Acad. Sci. USSR 303, 1508-1511.
8. Pevzner, P.A. 1989. 1-tuple DNA sequencing: Computer analysis. Journ. Biomolecul. Struct. & Dynamics 7(1), 63-73.
9. Pevzner, P.A., and Lipshutz, R.J. 1994. Towards DNA-sequencing by hybridization. 19th Symp. on Mathem. Found. of Comp. Sci., LNCS-841 143-258.
10. Pevzner, P.A., Lysov, Yu. P., Khrapko, K.R., Belyavsky, A.V., Florentiev, V.L., and Mirzabekov, A.D. 1991. Improved chips for sequencing by hybridization. Journ. Biomolecul. Struct. & Dynamics 9(2), 399-410.
11. Waterman, M.S. 1995. Introduction to Computational Biology. Chapman and Hall, London.