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Volumn 14, Issue 6, 2007, Pages 856-872

A study of accessible motifs and RNA folding complexity

Author keywords

Average case complexity; Binding sites; Dynamic programming; Optimal solution; RNA folding

Indexed keywords

MESSENGER RNA; MICRORNA;

EID: 34547700155     PISSN: 10665277     EISSN: None     Source Type: Journal    
DOI: 10.1089/cmb.2007.R020     Document Type: Conference Paper
Times cited : (58)

References (44)
  • 3
    • 0037388094 scopus 로고    scopus 로고
    • Genome-wide analysis of mRNA translation profiles in Saccharomyces cerevisiae
    • Arava, Y., Wang, Y., Storey, J., et al. 2003. Genome-wide analysis of mRNA translation profiles in Saccharomyces cerevisiae. Proc. Natl. Acad. Sci. USA 100, 3889-3894.
    • (2003) Proc. Natl. Acad. Sci. USA , vol.100 , pp. 3889-3894
    • Arava, Y.1    Wang, Y.2    Storey, J.3
  • 4
    • 0011883768 scopus 로고
    • Application of computational technologies to ribozyme biotechnology products
    • Christofferson, R., et al. 1994. Application of computational technologies to ribozyme biotechnology products. J. Mol. Struct. 311, 273.
    • (1994) J. Mol. Struct , vol.311 , pp. 273
    • Christofferson, R.1
  • 6
    • 0032727991 scopus 로고    scopus 로고
    • Themes in RNA-protein recognition
    • Draper, D. 1999. Themes in RNA-protein recognition. J. Mol. Biol. 293, 255-270.
    • (1999) J. Mol. Biol , vol.293 , pp. 255-270
    • Draper, D.1
  • 8
    • 36849111485 scopus 로고
    • Shape of a self-avoiding walk or polymer chain
    • Fisher, M. 1966. Shape of a self-avoiding walk or polymer chain. JCP 44, 616-622.
    • (1966) JCP , vol.44 , pp. 616-622
    • Fisher, M.1
  • 9
    • 0024641218 scopus 로고
    • Speeding up dynamic programming with applications to molecular biology
    • Galil, Z., and Giancarlo, R. 1989. Speeding up dynamic programming with applications to molecular biology. Theoret. Comput. Sci. 64, 107-118.
    • (1989) Theoret. Comput. Sci , vol.64 , pp. 107-118
    • Galil, Z.1    Giancarlo, R.2
  • 11
    • 0027507891 scopus 로고
    • Translational regulation of tra-2 by its 3′ untranslated region controls sexual identity in c. elegans
    • Goodwin, E., Okkema, P., Evans, T.C., et al. 1993. Translational regulation of tra-2 by its 3′ untranslated region controls sexual identity in c. elegans. Cell 75, 329-339.
    • (1993) Cell , vol.75 , pp. 329-339
    • Goodwin, E.1    Okkema, P.2    Evans, T.C.3
  • 13
    • 0032437667 scopus 로고    scopus 로고
    • Control of translation initiation in animals
    • Gray, N., and Wickens, M. 1998. Control of translation initiation in animals. Ann. Rev. Cell. Dev. Biol. 14, 399-458.
    • (1998) Ann. Rev. Cell. Dev. Biol , vol.14 , pp. 399-458
    • Gray, N.1    Wickens, M.2
  • 15
    • 0043123153 scopus 로고    scopus 로고
    • Vienna RNA secondary structure server
    • Hofacker, I.L. 2003. Vienna RNA secondary structure server. NAR 13, 3429-3431.
    • (2003) NAR , vol.13 , pp. 3429-3431
    • Hofacker, I.L.1
  • 16
    • 0035975193 scopus 로고    scopus 로고
    • Rational selection and quantitative evaluation of antisense oligonucleotides
    • Jayaraman, A., and Walton, S.P. 2001. Rational selection and quantitative evaluation of antisense oligonucleotides. Biochim. Biophys. Acta 1520, 105.
    • (2001) Biochim. Biophys. Acta , vol.1520 , pp. 105
    • Jayaraman, A.1    Walton, S.P.2
  • 17
    • 3543051100 scopus 로고    scopus 로고
    • A graph theoretical approach for predicting common RNA secondary structure motifs including pseudoknots in unaligned sequences
    • Ji, Y., Xu, X., and Stormo, G. 2004. A graph theoretical approach for predicting common RNA secondary structure motifs including pseudoknots in unaligned sequences. Bioinformatics 20, 1591-1602.
    • (2004) Bioinformatics , vol.20 , pp. 1591-1602
    • Ji, Y.1    Xu, X.2    Stormo, G.3
  • 19
    • 0034351060 scopus 로고    scopus 로고
    • Why is the DNA denaturation transition first order?
    • Kafri, Y., Mukamel, D., and Peliti, L. 2000. Why is the DNA denaturation transition first order? Phys. Rev. Lett. 85, 4988-4991.
    • (2000) Phys. Rev. Lett , vol.85 , pp. 4988-4991
    • Kafri, Y.1    Mukamel, D.2    Peliti, L.3
  • 20
    • 0013253286 scopus 로고
    • On-line dynamic programming with applications to the prediction of RNA secondary structure
    • Larmore, L., and Schieber, B. 1991. On-line dynamic programming with applications to the prediction of RNA secondary structure. J. Algorithms 12, 490-515.
    • (1991) J. Algorithms , vol.12 , pp. 490-515
    • Larmore, L.1    Schieber, B.2
  • 21
    • 33745803740 scopus 로고    scopus 로고
    • Quantification of the differences between quenched and annealed averaging for RNA secondary structures
    • Liu, T., and Bundschuh, R. 2005. Quantification of the differences between quenched and annealed averaging for RNA secondary structures. ArXiv Physics e-prints.
    • (2005) ArXiv Physics e-prints
    • Liu, T.1    Bundschuh, R.2
  • 22
    • 0037144457 scopus 로고    scopus 로고
    • Cleavage of scarecrow-like mRNA targets directed by a class of arabidopsis miRNA
    • Llave, C., et al. 2002. Cleavage of scarecrow-like mRNA targets directed by a class of arabidopsis miRNA. Science 297, 2053-2056.
    • (2002) Science , vol.297 , pp. 2053-2056
    • Llave, C.1
  • 23
    • 34547720153 scopus 로고    scopus 로고
    • Lyngsø, R.B., Zuker, M., and Pedersen, C.N.S. 1999. An improved algorithm for RNA secondary structure prediction [Technical Report RS-99-15]. BRICS.
    • Lyngsø, R.B., Zuker, M., and Pedersen, C.N.S. 1999. An improved algorithm for RNA secondary structure prediction [Technical Report RS-99-15]. BRICS.
  • 24
    • 0032729689 scopus 로고    scopus 로고
    • Predicting oligonucleotide affinity to nucleic acid target
    • Mathews, D., et al. 1999. Predicting oligonucleotide affinity to nucleic acid target. RNA 5, 1458-1469.
    • (1999) RNA , vol.5 , pp. 1458-1469
    • Mathews, D.1
  • 25
    • 0033591465 scopus 로고    scopus 로고
    • Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure
    • Mathews, D., Sabina, J., Zuker, M., et al. 1999. Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure. JMB 288, 911.
    • (1999) JMB , vol.288 , pp. 911
    • Mathews, D.1    Sabina, J.2    Zuker, M.3
  • 26
    • 0019082587 scopus 로고
    • Fast algorithm for predicting the secondary structure of single-stranded RNA
    • Nussinov, R., and Jacobson, A. 1980. Fast algorithm for predicting the secondary structure of single-stranded RNA. Proc. Natl. Acad. Sci. USA 77, 6309-6313.
    • (1980) Proc. Natl. Acad. Sci. USA , vol.77 , pp. 6309-6313
    • Nussinov, R.1    Jacobson, A.2
  • 27
    • 2942694026 scopus 로고    scopus 로고
    • An algorithm for finding conserved secondary structure motifs in unaligned RNA sequences
    • Pavesi, G., et al. 2004. An algorithm for finding conserved secondary structure motifs in unaligned RNA sequences. NAR 32, 3258-3269.
    • (2004) NAR , vol.32 , pp. 3258-3269
    • Pavesi, G.1
  • 28
    • 15244354492 scopus 로고    scopus 로고
    • Incorporating structure to predict microRNA targets
    • Robins, H., et al. 2005. Incorporating structure to predict microRNA targets. Proc. Natl. Acad. Sci. USA 102, 4006-4009.
    • (2005) Proc. Natl. Acad. Sci. USA , vol.102 , pp. 4006-4009
    • Robins, H.1
  • 29
    • 0029165020 scopus 로고
    • mRNA stability in mammalian cells
    • Ross, J. 1995. mRNA stability in mammalian cells. Microbiol. Rev. 59, 423-450.
    • (1995) Microbiol. Rev , vol.59 , pp. 423-450
    • Ross, J.1
  • 30
    • 0000900670 scopus 로고    scopus 로고
    • Spelling approximate or repeated motifs using a suffix tree
    • Sagot, M. 1998. Spelling approximate or repeated motifs using a suffix tree. LNCS, 111-127.
    • (1998) LNCS , pp. 111-127
    • Sagot, M.1
  • 31
    • 0033860727 scopus 로고    scopus 로고
    • Rational selection of antisense oligonucleotide sequences
    • Smith, L., et al. 2000. Rational selection of antisense oligonucleotide sequences. Eur. J. Pharm. Sci. 11, 191.
    • (2000) Eur. J. Pharm. Sci , vol.11 , pp. 191
    • Smith, L.1
  • 32
    • 0037224921 scopus 로고    scopus 로고
    • Framework for RNA silencing in plants
    • Tang, G., et al. 2003. Framework for RNA silencing in plants. Genes Dev. 17, 49-63.
    • (2003) Genes Dev , vol.17 , pp. 49-63
    • Tang, G.1
  • 33
    • 0005822936 scopus 로고
    • Improved estimation of secondary structure in ribonucleic acids
    • Tinoco, I., et al. 1973. Improved estimation of secondary structure in ribonucleic acids. Nature New Biol. 246, 40-41.
    • (1973) Nature New Biol , vol.246 , pp. 40-41
    • Tinoco, I.1
  • 34
    • 34547696651 scopus 로고    scopus 로고
    • Lattice Models of Polymers
    • Cambridge University Press, New York
    • Vanderzande, C. 1998. Lattice Models of Polymers (Cambridge Lecture Notes in Physics 11). Cambridge University Press, New York.
    • (1998) Cambridge Lecture Notes in Physics , vol.11
    • Vanderzande, C.1
  • 35
    • 0006572674 scopus 로고
    • Rapid dynamic programming algorithms for RNA secondary structure
    • Waterman, M., and Smith, T. 1986. Rapid dynamic programming algorithms for RNA secondary structure. Adv. Appl. Math. 7, 455-464.
    • (1986) Adv. Appl. Math , vol.7 , pp. 455-464
    • Waterman, M.1    Smith, T.2
  • 36
    • 0022535308 scopus 로고
    • Translational control of insulin biosynthesis
    • Welsh, M., Scherberg, N., Gilmore, R., et al. 1986. Translational control of insulin biosynthesis. Biochem. J. 235, 459-467.
    • (1986) Biochem. J , vol.235 , pp. 459-467
    • Welsh, M.1    Scherberg, N.2    Gilmore, R.3
  • 37
    • 0242669945 scopus 로고    scopus 로고
    • Regulation of mRNA translation by 5′- and 3′-utr-binding factors
    • Wilkie, G., Dickson, K., and Gray, N. 2003. Regulation of mRNA translation by 5′- and 3′-utr-binding factors. Trends Biochem. Sci. 28, 182-188.
    • (2003) Trends Biochem. Sci , vol.28 , pp. 182-188
    • Wilkie, G.1    Dickson, K.2    Gray, N.3
  • 38
    • 0041523923 scopus 로고    scopus 로고
    • Decay rates of human mRNAs: Correlation with functional characteristics and sequence attributes
    • Yang, E., et al. 2003. Decay rates of human mRNAs: correlation with functional characteristics and sequence attributes. Genome Res. 13, 1863-1872.
    • (2003) Genome Res , vol.13 , pp. 1863-1872
    • Yang, E.1
  • 39
    • 34547721628 scopus 로고    scopus 로고
    • Sequence motifs in ranked expression data. 1st RECOMB Satellite Workshop on Regul
    • Zilberstein, C., Eskin, E., and Yakhini, Z. 2004. Sequence motifs in ranked expression data. 1st RECOMB Satellite Workshop on Regul. Genomics, 264-275.
    • (2004) Genomics , pp. 264-275
    • Zilberstein, C.1    Eskin, E.2    Yakhini, Z.3
  • 40
    • 26444467747 scopus 로고    scopus 로고
    • A high-throughput approach for associating microRNAs with their activity conditions
    • Zilberstein, C., Ziv-Ukelson, M., Pinter, R.Y., et al. 2005. A high-throughput approach for associating microRNAs with their activity conditions. RECOMB 2005, 133-151.
    • (2005) RECOMB 2005 , pp. 133-151
    • Zilberstein, C.1    Ziv-Ukelson, M.2    Pinter, R.Y.3
  • 41
    • 0028900073 scopus 로고
    • The nonamer uuauuuauu is the key au-rich sequence motif that mediates mRNA degradation
    • Zubiaga, A., Belasco, J., and Greenberg, M. 1995. The nonamer uuauuuauu is the key au-rich sequence motif that mediates mRNA degradation. Mol. Cell. Biol. 15, 2219-2230.
    • (1995) Mol. Cell. Biol , vol.15 , pp. 2219-2230
    • Zubiaga, A.1    Belasco, J.2    Greenberg, M.3
  • 42
    • 0024806949 scopus 로고
    • Computer prediction of RNA structure
    • Zuker, M. 1989. Computer prediction of RNA structure. Methods Enzymol. 180, 262-288.
    • (1989) Methods Enzymol , vol.180 , pp. 262-288
    • Zuker, M.1
  • 43
    • 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. NAR 13, 3406-3415.
    • (2003) NAR , vol.13 , pp. 3406-3415
    • Zuker, M.1
  • 44
    • 0019876473 scopus 로고
    • Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information
    • Zuker, M., and Stiegler, P. 1981. Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information. NAR 9, 133-148.
    • (1981) NAR , vol.9 , pp. 133-148
    • Zuker, M.1    Stiegler, P.2


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