A gene-specific DNA sequencing chip for exploring molecular evolutionary change

Nucleic Acids Research

Volumn 32, Issue 3, 2004, Pages 1208-1213

  Fedrigo, Olivier ^b   Naylor, Gavin ^a  

^a FLORIDA STATE UNIVERSITY   (United States)

^b IOWA STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CYTOCHROME B; DNA; OLIGONUCLEOTIDE;

ARTICLE; CARNIVORE; COMPUTER MODEL; COMPUTER SIMULATION; CONTROLLED STUDY; DNA BINDING; DNA HYBRIDIZATION; DNA MICROARRAY; DNA SEQUENCE; DOLPHIN; FISH; GENE TARGETING; GENE TECHNOLOGY; GENETIC CODE; LAGOMORPH; MATHEMATICAL COMPUTING; MOLECULAR EVOLUTION; OLIGONUCLEOTIDE PROBE; PRIMATE; PRIORITY JOURNAL; RELIABILITY; RODENT; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS; SHARK; WHALE; ALGORITHM; EVALUATION; GENETIC VARIABILITY; GENETICS; INSTRUMENTATION; METHODOLOGY; NUCLEOTIDE SEQUENCE;

ALGORITHMS; BASE SEQUENCE; COMPUTER SIMULATION; CYTOCHROMES B; EVOLUTION, MOLECULAR; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; OLIGONUCLEOTIDE PROBES; SEQUENCE ALIGNMENT; VARIATION (GENETICS);

EID: 2342641426     PISSN: 03051048     EISSN: None     Source Type: Journal    
DOI: 10.1093/nar/gkh210     Document Type: Article

References (19)

1. Hunkapiller,T., Kaiser,R.J., Koop,B.F. and Hood,L. (1991) Large-scale and automated DNA sequence determination. Science, 254, 59-67.
2. Bains,W. and Smith,G.C. (1998) A novel method for nucleic acid sequence determination. J. Theor. Biol., 135, 303-307.
3. Lysov,Y.P., Florentiev,V.L., Khorlon,A.A. Khrapko,K.R., Shik,V.V. and Mirzakebov,A.D. (1988) Sequencing by hybridization via oligonucleotides. Dokl. Acad. Nauk SSSR, 303, 1508-1511.
4. Drmanac,R., Labat,I., Brukner,I. and Crkvenjakov,R. (1989) Sequencing of megabase plus DNA by hybridization: theory of the method. Genomics, 4, 114-128.
5. Southern,E.M. (1996) DNA chips: analysing sequence by hybridization to oligonucleotides on a large scale. Trends Genet., 12, 110-115.
6. Wallace,R.B., Shaffer,J., Murphy,R.E., Bonner,J., Hiros,T. and Itakura,K. (1979) Hybridization of synthetic oligodeoxyribonucleotides to X174 DNA: the effect of a single base pair mismatch. Nucleic Acids Res., 6, 3543-3557.
7. Thein,S.L. and Wallace,R.B. (1986) The use of synthetic oligonucleotides as specific hybridization probes in the diagnosis of genetic disorders. In Davies,E.K. (ed.), Human Genetic Disease: A Practical Approach. IRL Press, Oxford, UK, pp. 33-50.
8. Wallraff,G., Labadie,J., Brock,P., Dipietro,R., Nguyen,T., Huynh,T., Hinsberg,W. and McGall,G. (1997) DNA sequencing on a chip. Chemtech, 27, 22-32.
9. Preparata,F.P., Fireze,A.M. and Upfal,E. (1999) On the power of universal bases in sequencing by hybridization. In Recomb'99: Proceedings of the Third Annual International Conference on Computational Molecular Biology. Lyon, France, pp. 295-301.
10. Pevzner,P.A., Lysov,Y.P., Khrapko,K.R., Belvavsky,A.V., Florentiev,V.L. and Mirzabekov,A.D. (1991) Improved chips for sequencing by hybridization. J. Biomol. Struct. Dynam., 9, 399-410.
11. Winzeler,E.A., Richards,D.R., Conway,A.R., Goldstein,A.L., Kalman,S., McCullough,M.J., McCusker,J.H., Stevens,D.A., Wodicka,L., Lockhart,D.J. and Davis,R.W. (1998) Direct allelic variation scanning of the yeast genome. Science, 281, 1194-1197.
12. Southern,E.M., Maskos,U. and Elder,J.K. (1992) Analyzing and comparing nucleic acid sequences by hybridization to arrays of oligonucleotides: evaluation using experimental models. Genomics, 13, 1008-1017.
13. Sakarovitch,M. (1984) Optimisation Combinatoire: Méthodes Mathématiques et Algorithmiques. Collection Enseignement des Sciences, Hermann, Paris.
14. Cook,W.J., Cunningham,W.H., Pulleyblank,W.R. and Schrijver,A. (1998) Combinatorial Optimization. Wiley-Interscience Series in Discrete Mathematics and Optimization. Wiley, New York.
15. Cormen,T.H., Leiserson,C.E. and Rivest,R.L. (1997) Introduction to Algorithms. MIT Press. McGraw-Hill Book Co.
16. Thomson,J.D., Higgins,D.G. and Gibson,T.J. (1994) ClustalW: improving the sensivity of progressive multiple alignment through sequence weighting, position, gap penalties and weight matrix choice. Nucleic Acids Res., 22, 4673-4680.
17. Hacia,J., Brody,L., Chee,M., Fodor,S. and Collins,F. (1996) Detection of heterozygous mutation in BRCA1 using high density oligonucleotide array and two-colour fluorescence analysis. Nature Genet., 14, 441-447.
18. Ramsay,G. (1998) DNA chips: state-of-the art. Nat. Biotechnol., 16, 40-44.
19. Naylor,G.J.P. and Gerstein,M. (2000) Measuring shifts in function and evolutionary opportunity using variability profiles: a case study of the globins. J. Mol. Evol., 51, 223-233.