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Volumn 453, Issue , 2008, Pages 3-31

UNAFold: Software for nucleic acid folding and hybridization

Author keywords

Free energy minimization; Melting temperature; Nucleic acid hybridization; Nucleic acid melting profiles (or DNA melting profiles); Partition functions; RNA folding

Indexed keywords

INSECTIVORA;

EID: 84934438960     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-60327-429-6_1     Document Type: Article
Times cited : (858)

References (37)
  • 1
    • 0003787146 scopus 로고
    • Princeton University Press, Princeton, NJ
    • Bellman, R. E. (1957) Dynamic Programming. Princeton University Press, Princeton, NJ.
    • (1957) Dynamic Programming
    • Bellman, R.E.1
  • 2
    • 0018254569 scopus 로고
    • RNA secondary structure: A complete mathematical analysis
    • Waterman, M. S., Smith, T. F. (1978) RNA secondary structure: a complete mathematical analysis. Math Biosci 42, 257-266.
    • (1978) Math Biosci , vol.42 , pp. 257-266
    • Waterman, M.S.1    Smith, T.F.2
  • 3
    • 0001509501 scopus 로고
    • Secondary structure of single-stranded nucleic acids
    • Rota, G.-C, ed, Academic Press, New York
    • Waterman, M. S. (1978) Secondary structure of single-stranded nucleic acids, in (Rota, G.-C., ed.), Studies in Foundations and Combinatorics, Academic Press, New York.
    • (1978) Studies in Foundations and Combinatorics
    • Waterman, M.S.1
  • 4
    • 0019321678 scopus 로고
    • Some rules for ordering nucleotides in DNA
    • Nussinov, R. (1980) Some rules for ordering nucleotides in DNA. Nucleic Acids Res 8, 4545-4562.
    • (1980) Nucleic Acids Res , vol.8 , pp. 4545-4562
    • Nussinov, R.1
  • 5
    • 0019876473 scopus 로고
    • Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information
    • Zuker, M., Stiegler, P. (1981) Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information. Nucleic Acids Res 9, 133-148.
    • (1981) Nucleic Acids Res , vol.9 , pp. 133-148
    • Zuker, M.1    Stiegler, P.2
  • 7
    • 0001947120 scopus 로고
    • The use of dynamic programming algorithms in RNA secondary structure prediction
    • Waterman, M. S, ed, CRC Press, Boca Raton, FL
    • Zuker, M. (1989) The use of dynamic programming algorithms in RNA secondary structure prediction, in (Waterman, M. S., ed.), Mathematical Methods for DNA Sequences. CRC Press, Boca Raton, FL.
    • (1989) Mathematical Methods for DNA Sequences
    • Zuker, M.1
  • 8
    • 0001499835 scopus 로고
    • Prediction of RNA secondary structure by energy minimization
    • Griffin, A. M, Griffin, H. G, eds, Humana Press, Totowa, NJ
    • Zuker, M. (1994) Prediction of RNA secondary structure by energy minimization, in (Griffin, A. M., Griffin, H. G., eds.), Computer Analysis of Sequence Data,. Humana Press, Totowa, NJ.
    • (1994) Computer Analysis of Sequence Data
    • Zuker, M.1
  • 9
    • 0002287019 scopus 로고    scopus 로고
    • Algorithms and thermodynamics for RNA secondary structure prediction: A practical guide
    • Barciszewski J, Clark, B. F. C, eds, Kluwer, Dordrecht
    • Zuker, M., Mathews, D. H., Turner, D. H. (1999) Algorithms and thermodynamics for RNA secondary structure prediction: a practical guide, in (Barciszewski J., Clark, B. F. C., eds.), RNA Biochemistry and Biotechnology. Kluwer, Dordrecht.
    • (1999) RNA Biochemistry and Biotechnology
    • Zuker, M.1    Mathews, D.H.2    Turner, D.H.3
  • 10
    • 0042121256 scopus 로고    scopus 로고
    • Mfold web server for nucleic acid folding and hybridization prediction
    • Zuker, M. (2003) Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res 31, 3406-3415.
    • (2003) Nucleic Acids Res , vol.31 , pp. 3406-3415
    • Zuker, M.1
  • 11
    • 34249772381 scopus 로고
    • Fast folding and comparison of RNA secondary structures
    • Hofacker, I. L., Fontana, W., Stadler, P.F., et al. (1994) Fast folding and comparison of RNA secondary structures. Monatsh Chem 125, 167-188.
    • (1994) Monatsh Chem , vol.125 , pp. 167-188
    • Hofacker, I.L.1    Fontana, W.2    Stadler, P.F.3
  • 12
    • 0033080745 scopus 로고    scopus 로고
    • Complete suboptimal folding of RNA and the stability of secondary structures
    • Wuchty, S., Fontana, W., Hofacker, I. L., et al. (1999) Complete suboptimal folding of RNA and the stability of secondary structures. Biopolymers 49, 145-165.
    • (1999) Biopolymers , vol.49 , pp. 145-165
    • Wuchty, S.1    Fontana, W.2    Hofacker, I.L.3
  • 13
    • 0043123153 scopus 로고    scopus 로고
    • Vienna RNA secondary structure server
    • Hofacker, I. L. (2003) Vienna RNA secondary structure server. Nucleic Acids Res 31, 3429-3431.
    • (2003) Nucleic Acids Res , vol.31 , pp. 3429-3431
    • Hofacker, I.L.1
  • 14
    • 0025264854 scopus 로고
    • The equilibrium partition function and base pair binding probabilities for RNA secondary structure
    • McCaskill, J. S. (1990) The equilibrium partition function and base pair binding probabilities for RNA secondary structure. Biopolymers 29, 1105-1119.
    • (1990) Biopolymers , vol.29 , pp. 1105-1119
    • McCaskill, J.S.1
  • 15
    • 0035283171 scopus 로고    scopus 로고
    • Statistical prediction of single-stranded regions in RNA secondary structure and application to predicting effective antisense target sites and beyond
    • Ding, Y., Lawrence, C. E. (2001) Statistical prediction of single-stranded regions in RNA secondary structure and application to predicting effective antisense target sites and beyond. Nucleic Acids Res 29, 1034-1046.
    • (2001) Nucleic Acids Res , vol.29 , pp. 1034-1046
    • Ding, Y.1    Lawrence, C.E.2
  • 16
    • 0346888665 scopus 로고    scopus 로고
    • A statistical sampling algorithm for RNA secondary structure prediction
    • Ding, Y., Lawrence, C. E. (2003) A statistical sampling algorithm for RNA secondary structure prediction. Nucleic Acids Res 31, 7280-7301.
    • (2003) Nucleic Acids Res , vol.31 , pp. 7280-7301
    • Ding, Y.1    Lawrence, C.E.2
  • 17
    • 3242877996 scopus 로고    scopus 로고
    • Sfold web server for statistical folding and rational design of nucleic acids
    • Ding, Y., Lawrence, C. E. (2004) Sfold web server for statistical folding and rational design of nucleic acids. Nucleic Acids Res 32, W135-W141.
    • (2004) Nucleic Acids Res , vol.32
    • Ding, Y.1    Lawrence, C.E.2
  • 18
    • 0030875847 scopus 로고    scopus 로고
    • Thermodynamics and NMR of internal GT mismatches in DNA
    • Allawi, H. A., SantaLucia, J. Jr. (1997) Thermodynamics and NMR of internal GT mismatches in DNA. Biochemistry 36, 10581-10594.
    • (1997) Biochemistry , vol.36 , pp. 10581-10594
    • Allawi, H.A.1    SantaLucia Jr., J.2
  • 19
    • 0032539693 scopus 로고    scopus 로고
    • A unified view of polymer, dumbell, and oligonucleotide DNA nearest-neighbor thermodynamics
    • SantaLucia, J. Jr. (1998) A unified view of polymer, dumbell, and oligonucleotide DNA nearest-neighbor thermodynamics. Proc Natl Acad Sci U S A 95, 1460-1465.
    • (1998) Proc Natl Acad Sci U S A , vol.95 , pp. 1460-1465
    • SantaLucia Jr., J.1
  • 20
    • 3042599013 scopus 로고    scopus 로고
    • The thermodynamics of DNA structural motifs
    • SantaLucia, J. Jr., Hicks, D. (2004) The thermodynamics of DNA structural motifs. Annu Rev Biophys Biom 33, 415-440.
    • (2004) Annu Rev Biophys Biom , vol.33 , pp. 415-440
    • SantaLucia Jr., J.1    Hicks, D.2
  • 21
    • 27744491204 scopus 로고    scopus 로고
    • Competitive hybridization kinetics reveals unexpected behavior patterns
    • Zhang, Y., Hammer, D. A., Graves, D. J. (2005) Competitive hybridization kinetics reveals unexpected behavior patterns. Biophys J 89, 2950-2959.
    • (2005) Biophys J , vol.89 , pp. 2950-2959
    • Zhang, Y.1    Hammer, D.A.2    Graves, D.J.3
  • 23
    • 85069260000 scopus 로고
    • Absorbance melting curves of RNA
    • Dahlberg, J. E, Abelson, J. N. eds, Academic Press, New York
    • Puglisi, J. D., Tinoco, I. Jr. (1989) Absorbance melting curves of RNA, in (Dahlberg, J. E., Abelson, J. N. eds.), RNA Processing Part A: General Methods. Academic Press, New York.
    • (1989) RNA Processing Part A: General Methods
    • Puglisi, J.D.1    Tinoco Jr., I.2
  • 24
    • 18444386491 scopus 로고    scopus 로고
    • RNAML: A standard syntax for exchanging RNA information
    • Waugh, A., Gendron, P., Altman, R., et al. (2002) RNAML: a standard syntax for exchanging RNA information. RNA 8, 707-717.
    • (2002) RNA , vol.8 , pp. 707-717
    • Waugh, A.1    Gendron, P.2    Altman, R.3
  • 25
    • 0032901515 scopus 로고    scopus 로고
    • Isothermal titration calorimetry and differential scanning calorimetry as complementary tools to investigate the energetics of biomolecular recognition
    • Jelesarov, I., Bosshard, H. R. (1999) Isothermal titration calorimetry and differential scanning calorimetry as complementary tools to investigate the energetics of biomolecular recognition. J Mol Recog 12, 3-18.
    • (1999) J Mol Recog , vol.12 , pp. 3-18
    • Jelesarov, I.1    Bosshard, H.R.2
  • 26
    • 0028000994 scopus 로고
    • Coaxial stacking of helixes enhances binding of oligoribonucleotides and improves predictions of RNA
    • Walter, A. E., Turner, D. H., Kim, J., et al. (1994) Coaxial stacking of helixes enhances binding of oligoribonucleotides and improves predictions of RNA. Proc Natl Acad Sci U S A 91, 9218-9222.
    • (1994) Proc Natl Acad Sci U S A , vol.91 , pp. 9218-9222
    • Walter, A.E.1    Turner, D.H.2    Kim, J.3
  • 27
    • 0033591465 scopus 로고    scopus 로고
    • Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure
    • Mathews, D. H., Sabina, J., Zuker, M., et al. (1999) Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure. J Mol Biol 288:911-940.
    • (1999) J Mol Biol , vol.288 , pp. 911-940
    • Mathews, D.H.1    Sabina, J.2    Zuker, M.3
  • 28
    • 0030829855 scopus 로고    scopus 로고
    • RnaViz2, a program for the visualisation of RNA secondary structure
    • De Rijk, P., De Wachter, R. (1997) RnaViz2, a program for the visualisation of RNA secondary structure. Nucleic Acids Res 25, 4679-4684.
    • (1997) Nucleic Acids Res , vol.25 , pp. 4679-4684
    • De Rijk, P.1    De Wachter, R.2
  • 29
    • 0037314114 scopus 로고    scopus 로고
    • RnaViz2: An improved representation of RNA secondary structure
    • De Rijk, P., De Wachter, R. (2003) RnaViz2: an improved representation of RNA secondary structure. Bioinformatics 19, 299-300.
    • (2003) Bioinformatics , vol.19 , pp. 299-300
    • De Rijk, P.1    De Wachter, R.2
  • 30
    • 0036493198 scopus 로고    scopus 로고
    • Compilation and analysis of group II intron insertions in bacterial genomes: Evidence for retroelement behavior
    • Dai, L. Zimmerly, S. (2002) Compilation and analysis of group II intron insertions in bacterial genomes: evidence for retroelement behavior. Nucleic Acids Res 30, 1091-1102.
    • (2002) Nucleic Acids Res , vol.30 , pp. 1091-1102
    • Dai, L.1    Zimmerly, S.2
  • 31
    • 0034910710 scopus 로고    scopus 로고
    • Coevolution of group II intron RNA structures with their intron-encoded reverse transcriptases
    • Toor, N., Hausner, G., Zimmerly, S. (2001) Coevolution of group II intron RNA structures with their intron-encoded reverse transcriptases. RNA 7, 1142-1152.
    • (2001) RNA , vol.7 , pp. 1142-1152
    • Toor, N.1    Hausner, G.2    Zimmerly, S.3
  • 32
    • 0024428420 scopus 로고
    • Comparative and functional anatomy of group II catalytic introns: A review
    • Michel, F., Umesono, K., Ozeki, H. (1989) Comparative and functional anatomy of group II catalytic introns: a review. Gene 82, 5-30.
    • (1989) Gene , vol.82 , pp. 5-30
    • Michel, F.1    Umesono, K.2    Ozeki, H.3
  • 33
    • 0031745782 scopus 로고    scopus 로고
    • Using reliability information to annotate RNA secondary structures
    • Zuker, M., Jacobson, A. B. (1998) Using reliability information to annotate RNA secondary structures. RNA 4, 669-679.
    • (1998) RNA , vol.4 , pp. 669-679
    • Zuker, M.1    Jacobson, A.B.2
  • 34
    • 0032579197 scopus 로고    scopus 로고
    • Structural plasticity in RNA and its role in the regulation of protein translation in coliphage qβ
    • Jacobson, A. B., Arora, R., Zuker, M., et al. (1998) Structural plasticity in RNA and its role in the regulation of protein translation in coliphage qβ. J Mol Biol 275, 589-600.
    • (1998) J Mol Biol , vol.275 , pp. 589-600
    • Jacobson, A.B.1    Arora, R.2    Zuker, M.3
  • 35
    • 3342977915 scopus 로고    scopus 로고
    • Using an RNA secondary structure partition function to determine confidence in base pairs predicted by free energy minimization
    • Mathews, D. H. (2004) Using an RNA secondary structure partition function to determine confidence in base pairs predicted by free energy minimization. RNA 10, 1174-1177.
    • (2004) RNA , vol.10 , pp. 1174-1177
    • Mathews, D.H.1
  • 36
    • 23144440350 scopus 로고    scopus 로고
    • DINAMelt web server for nucleic acid melting prediction
    • Markham, N. R., Zuker, M. (2005) DINAMelt web server for nucleic acid melting prediction. Nucleic Acids Res 33, W577-W581.
    • (2005) Nucleic Acids Res , vol.33
    • Markham, N.R.1    Zuker, M.2
  • 37
    • 0029670262 scopus 로고    scopus 로고
    • Molecular beacons: Probes that fluoresce upon hybridization
    • Tyagi, S., Kramer, F. R. (1996) Molecular beacons: probes that fluoresce upon hybridization. Nat Biotechnol 4, 303-308.
    • (1996) Nat Biotechnol , vol.4 , pp. 303-308
    • Tyagi, S.1    Kramer, F.R.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.