Selecting signature oligonucleotides to identify organisms using DNA arrays

Bioinformatics

Volumn 18, Issue 10, 2002, Pages 1340-1349

  Kaderali, Lars ^a   Schliep, Alexander ^b  

^a UNIVERSITY OF COLOGNE   (Germany)

^b MAX PLANCK INSTITUTE FOR MOLECULAR GENETICS   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

BASE; OLIGONUCLEOTIDE; RIBOSOME DNA; RNA 28S;

ALGORITHM; ANALYTIC METHOD; ARTICLE; BASE PAIRING; COMPUTER PROGRAM; CONTROLLED STUDY; DNA MICROARRAY; DNA SEQUENCE; HUMAN IMMUNODEFICIENCY VIRUS 1; MATHEMATICAL MODEL; MELTING POINT; NONHUMAN; OLIGONUCLEOTIDE PROBE; PRIORITY JOURNAL; SEQUENCE ALIGNMENT; VIRUS IDENTIFICATION; VIRUS TYPING; BIOLOGICAL MODEL; CHEMICAL MODEL; CHEMISTRY; CLASSIFICATION; COMPUTER AIDED DESIGN; COMPUTER SIMULATION; DNA PROBE; EQUIPMENT DESIGN; EVALUATION; GENE TARGETING; GENETICS; HUMAN; INSTRUMENTATION; METHODOLOGY; MICROBIOLOGICAL EXAMINATION; MOLECULAR GENETICS; NUCLEIC ACID DATABASE; NUCLEOTIDE SEQUENCE; QUALITY CONTROL; REPRODUCIBILITY; SENSITIVITY AND SPECIFICITY; TEMPERATURE;

HUMAN IMMUNODEFICIENCY VIRUS; HUMAN IMMUNODEFICIENCY VIRUS 1; OTHER SEQUENCES; RNA VIRUSES;

ALGORITHMS; BASE SEQUENCE; COMPUTER SIMULATION; COMPUTER-AIDED DESIGN; DATABASES, NUCLEIC ACID; DNA PROBES; EQUIPMENT DESIGN; GENE TARGETING; HIV-1; HUMANS; MICROBIOLOGICAL TECHNIQUES; MODELS, CHEMICAL; MODELS, GENETIC; MOLECULAR SEQUENCE DATA; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; QUALITY CONTROL; REPRODUCIBILITY OF RESULTS; RNA, RIBOSOMAL, 28S; SENSITIVITY AND SPECIFICITY; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA; TEMPERATURE;

EID: 0036772248     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/18.10.1340     Document Type: Article

References (36)

1. Allawi,H. and SantaLucia,J. (1997) Thermodynamics and NMR of internal g-t mismatches in DNA. Biochemistry, 36, 10581-10594.
2. Allawi,H. and SantaLucia,J. (1998a) Nearest neighbor parameters for internal g-a mismatches in DNA. Biochemistry, 37, 2170-2179.
3. Allawi,H. and SantaLucia,J. (1998b) Nearest neighbor parameters of internal a-c mismatches in DNA: sequence dependence and pH effects. Biochemistry, 37, 9435-9444.
4. Allawi,H. and SantaLucia,J. (1998c) Thermodynamics and NMR of internal c-t mismatches in DNA. Nucleic Acids Res., 26, 2694-2701.
5. Bommarito,S., Peyret,N. and SantaLucia Jr,J. (2000) Thermodynamic parameters for DNA sequences with dangling ends. Nucleic Acids Res., 28, 1929-1934.
6. Breslauer,K., Frank,R., Blöcker,H. and Marky,L. (1986) Predicting DNA duplex stability from the base sequence. Proc. Natl Acad. Sci. USA, 83, 3746-3750.
7. Cupal,J. (1997) The density of states of RNA secondary structures, Master's thesis, University of Vienna.
8. Delpech,M. (2000) Les puces à ADN. Annales de Biologie Clinique, 58, 29-38.
9. Durbin,R., Eddy,S., Krogh,A. and Mitchison,G. (1998) Biological Sequence Analysis. Cambridge University Press, Cambridge.
10. Fox,G.E. (2000) Rapid identification of unexpected bacteria pathogens in space environments. http://www.isso.uh.edu/publications/A9900/html/mini/mini-fox.htm.
11. Freier,S., Kierzek,R., Jaeger,J., Sugimoto,N., Caruthers,M., Neilson,T. and Turner,D. (1986) Improved free-energy parameters for predictions of RNA duplex stability. Proc. Natl Acad. Sci. USA, 83, 9373-9377.
12. Gotoh,O. and Tagashira,Y. (1981) Stabilities of nearest-neighbor doublets in double-helical DNA determined by fitting calculated melting profiles to observed profiles. Biopolymers, 20, 1033-1042.
13. Gray,D. (1997) Derivation of nearest-neighbor properties from data on nucleic acid oligomers. II. thermodynamic parameters of DNA-RNA hybrids and DNA duplexes. Biopolymers, 42, 795-810.
14. Gusfield,D. (1997) Algorithms on Strings, Trees, and Sequences. Computer Science and Computational Biology. Cambridge University Press, Cambridge.
15. Kaderali,L. (2001) Selecting target specific probes for DNA arrays, Master's thesis, University of Cologne.
16. Ke,S. and Wartell,R. (1995) Influence of neighboring base pairs on the stability of single base bulges and base pairs in a DNA fragment. Biochemistry, 34, 4593-4600.
17. Knill,E.H., Schliep,A. and Torney,D.C. (1996) Interpretation of pooling experiments using the Markov chain Monte Carlo method. J. Comput. Biol., 3, 395-406.
18. Kurtz,S., Choudhuri,J., Ohlebusch,E., Schleiermacher,C., Stoye,J. and Giegerich,R. (2001) Reputer: the manifold applications of repeat analysis on a genomic scale. Nucleic Acids Res., 29, 4633-4642.
19. LANL, (1999) HIV sequence database - 1999 HIV-1 subtype reference alignments. Los Alamos National Laboratories,http://hiv-web.lanl.gov/.
20. LeBlanc,D. and Morden,K. (1991) Thermodynamic characterization of deoxyribooligonucleotide duplexes containing bulges. Biochemistry, 30, 4042-4047.
21. Li,F. and Stormo,G. (2001) Selection of optimal DNA oligos for gene expression arrays. Bioinformatics, 17, 1067-1076.
22. Markmann,M. (2000) Entwicklung und Anwendung einer 28S rDNA-Sequenzdatenbank zur Aufschlüsselung der Artenvielfalt limnischer Meiobenthosfauna im Hinblick auf den Einsatz moderner Chiptechnologie, PhD thesis, University of Munich.
23. m and sequence of DNA duplexes with δh computed by an improved empirical potential method. Biopolymers, 22, 1979-2000.
24. Owczarzy.R., Vallone,P., Gallo,F., Paner,T., Lane,M. and Benight,A. (1997) Predicting sequence-dependent melting stability of short duplex DNA oligomers. Biopolymers, 44, 217-239.
25. Peyret,N., Seneviratne,P., Allawi,H. and SantaLucia,J. (1999) Nearest-neighbor thermodynamics and NMR of DNA sequences with internal a-a, c-c, g-g and t-t mismatches. Biochemistry, 38, 3468-3477.
26. Quartin,R. and Wetmur,J. (1989) Effect of ionic strength on the hybridization of oligonucleotides with reduced charge due to methylphosponate linkages to unmodified oligodeoxynucleotides containing the complementary sequence. Biochemistry, 28, 1040-1047.
27. Rychlik,W. and Rhoads,R. (1989) A computer program for choosing optimal oligonucleotides for filter hybridization, sequencing and in vitro amplification of DNA. Nucleic Acids Res., 17, 8543-8551.
28. SantaLucia,J. (1998) A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics. Proc. Natl Acad. Sci. USA, 95, 1460-1465.
29. SantaLucia Jr,J., Allawi,H. and Seneviratne,P. (1996) Improved nearest-neighbor parameters for predicting DNA duplex stability. Biochemistry, 35, 3555-3562.
30. SantaLucia Jr.,J. and Turner,D. (1997) Measuring the thermodynamics of RNA secondary structure formation. Biopolymers, 44, 309-319.
31. Sugimoto,N., Nakano,S., Yoneyama,M. and Honda,K. (1996) Improved thermodynamic parameters and helix initiation factor to predict stability of DNA duplexes. Nucleic Acids Res., 24, 4501-4505.
32. Turner,D. (1992) Bulges in nucleic acids. Curr. Opin. Struct. Biol., 2, 334-337.
33. Ukkonen,E. (1995) On-line . construction of suffix-trees. Algorithmica, 14, 249-260.
34. Waterman,M. (1995) Introduction to Computational Biology. Cambridge University Press, Cambridge.
35. Xia,T., SantaLucia,J., Burkard,M., Kierzyk,R., Schroeder,S., Jiao,X., Cox,C. and Turner,D. (1998) Thermodynamic parameters for an expanded nearest-neighbor model for formation of RNA duplexes with Watson-Crick base pairs. Biochemistry, 37, 14719-14735.
36. Zuker,M. (1989) On finding all suboptimal foldings of an RNA molecule. Science, 244, 48-52.