메뉴 건너뛰기




Volumn 27, Issue 4, 2011, Pages 456-463

RNA-RNA interaction prediction based on multiple sequence alignments

Author keywords

[No Author keywords available]

Indexed keywords

RNA;

EID: 79951537034     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btq659     Document Type: Article
Times cited : (36)

References (51)
  • 1
    • 0041940818 scopus 로고    scopus 로고
    • Dynamic programming algorithms for RNA secondary structure prediction with pseudoknots
    • Akutsu, T. (2000) Dynamic programming algorithms for RNA secondary structure prediction with pseudoknots. Disc. Appl. Math., 104, 45-62.
    • (2000) Disc. Appl. Math. , vol.104 , pp. 45-62
    • Akutsu, T.1
  • 2
    • 33645965588 scopus 로고    scopus 로고
    • RNA-RNA interaction prediction and antisense RNA target search
    • Alkan, C. et al. (2006) RNA-RNA interaction prediction and antisense RNA target search. J. Comput. Biol., 13, 267-282.
    • (2006) J. Comput. Biol. , vol.13 , pp. 267-282
    • Alkan, C.1
  • 3
    • 4644309196 scopus 로고    scopus 로고
    • The functions of animal microRNAs
    • Ambros, V. (2004) The functions of animal microRNAs. Nature, 431, 350-355.
    • (2004) Nature , vol.431 , pp. 350-355
    • Ambros, V.1
  • 4
    • 11844254846 scopus 로고    scopus 로고
    • Secondary structure prediction of interacting RNA molecules
    • Andronescu, M. et al. (2005) Secondary structure prediction of interacting RNA molecules. J. Mol. Biol., 345, 1101-1112.
    • (2005) J. Mol. Biol. , vol.345 , pp. 1101-1112
    • Andronescu, M.1
  • 5
    • 0034725539 scopus 로고    scopus 로고
    • fhlA repression by OxyS RNA: kissing complex formation at two sites results in a stable antisense-target RNA complex
    • Argaman, L. and Altuvia, S. (2000) fhlA repression by OxyS RNA: kissing complex formation at two sites results in a stable antisense-target RNA complex. J. Mol. Biol., 300, 1101-1112.
    • (2000) J. Mol. Biol. , vol.300 , pp. 1101-1112
    • Argaman, L.1    Altuvia, S.2
  • 6
    • 0036703184 scopus 로고    scopus 로고
    • The expanding snoRNA world
    • Bachellerie, J. et al. (2002) The expanding snoRNA world. Biochimie, 84, 775-779.
    • (2002) Biochimie , vol.84 , pp. 775-779
    • Bachellerie, J.1
  • 7
    • 33744979613 scopus 로고    scopus 로고
    • Partition function and base pairing probabilities of RNA heterodimers
    • Bernhart, S. et al. (2006) Partition function and base pairing probabilities of RNA heterodimers. Algorithms Mol. Biol., 1, 3.
    • (2006) Algorithms Mol. Biol. , vol.1 , pp. 3
    • Bernhart, S.1
  • 8
    • 58249121729 scopus 로고    scopus 로고
    • RNAalifold: improved consensus structure prediction for RNA alignments
    • Bernhart, S. et al. (2008) RNAalifold: improved consensus structure prediction for RNA alignments. BMC Bioinformatics, 9, 474-487.
    • (2008) BMC Bioinformatics , vol.9 , pp. 474-487
    • Bernhart, S.1
  • 9
    • 0029286626 scopus 로고
    • An element in human U6 RNA destabilizes the U4/U6 spliceosomal RNA complex
    • Brow, D. and Vidaver, R. (1995) An element in human U6 RNA destabilizes the U4/U6 spliceosomal RNA complex. RNA, 1, 122-131.
    • (1995) RNA , vol.1 , pp. 122-131
    • Brow, D.1    Vidaver, R.2
  • 10
    • 0036761417 scopus 로고    scopus 로고
    • RNA loop-loop interactions as dynamic functional motifs
    • Brunel, C. et al. (2003) RNA loop-loop interactions as dynamic functional motifs. Biochimie, 84, 925-944.
    • (2003) Biochimie , vol.84 , pp. 925-944
    • Brunel, C.1
  • 11
    • 57249083988 scopus 로고    scopus 로고
    • IntaRNA: efficient prediction of bacterial sRNA targets incorporating target site accessibility and seed regions
    • Busch, A. et al. (2008) IntaRNA: efficient prediction of bacterial sRNA targets incorporating target site accessibility and seed regions. Bioinformatics, 24, 2849-2856.
    • (2008) Bioinformatics , vol.24 , pp. 2849-2856
    • Busch, A.1
  • 13
    • 66349105749 scopus 로고    scopus 로고
    • A partition function algorithm for interacting nucleic acid strands
    • Chitsaz, H. et al. (2009b) A partition function algorithm for interacting nucleic acid strands. Bioinformatics, 25, i365-i373.
    • (2009) Bioinformatics , vol.25
    • Chitsaz, H.1
  • 14
    • 0346888665 scopus 로고    scopus 로고
    • Astatistical sampling algorithm for RNA secondary structure prediction
    • Ding, Y. and Lawrence, C.E. (2003)Astatistical sampling algorithm for RNA secondary structure prediction. Nucleic Acid Res., 31, 7280-7301.
    • (2003) Nucleic Acid Res. , vol.31 , pp. 7280-7301
    • Ding, Y.1    Lawrence, C.E.2
  • 15
    • 33847609597 scopus 로고    scopus 로고
    • Thermodynamic analysis of interacting nucleic acid strands
    • Dirks, R. et al. (2007) Thermodynamic analysis of interacting nucleic acid strands. SIAM Rev., 49, 65-88.
    • (2007) SIAM Rev. , vol.49 , pp. 65-88
    • Dirks, R.1
  • 16
    • 0029804708 scopus 로고    scopus 로고
    • Structural features of U6 snRNA and dynamic interactions with other spliceosomal components leading to pre-mRNA splicing
    • Forne, T. et al. (1996) Structural features of U6 snRNA and dynamic interactions with other spliceosomal components leading to pre-mRNA splicing. Biochimie, 78, 434-442.
    • (1996) Biochimie , vol.78 , pp. 434-442
    • Forne, T.1
  • 17
    • 0028823370 scopus 로고
    • An interactive framework forRNAsecondary structure prediction with a dynamical treatment of constraints
    • Gaspin, C. andWesthof, E. (1995)An interactive framework forRNAsecondary structure prediction with a dynamical treatment of constraints. J. Mol. Biol, 254, 163-174.
    • (1995) J. Mol. Biol. , vol.254 , pp. 163-174
    • Gaspin, C.1    Westhof, E.2
  • 18
    • 1542320707 scopus 로고    scopus 로고
    • Hfq, a new chaperoning role: binding to messenger RNA determines access for small RNA regulator
    • Geissmann, T. and Touati, D. (2004) Hfq, a new chaperoning role: binding to messenger RNA determines access for small RNA regulator. EMBO J., 23, 396-405.
    • (2004) EMBO J. , vol.23 , pp. 396-405
    • Geissmann, T.1    Touati, D.2
  • 19
    • 0037387973 scopus 로고    scopus 로고
    • A survey of small RNA-encoding genes in Escherichia coli
    • Hershberg, R. et al. (2003) A survey of small RNA-encoding genes in Escherichia coli. Nucleic Acids Res., 31, 1813-1820.
    • (2003) Nucleic Acids Res. , vol.31 , pp. 1813-1820
    • Hershberg, R.1
  • 20
    • 34249772381 scopus 로고
    • Fast folding and comparison of RNA secondary structures
    • Hofacker, I.L. 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
  • 21
    • 0036301332 scopus 로고    scopus 로고
    • Secondary structure prediction for aligned RNA sequences
    • Hofacker, I. et al. (2002) Secondary structure prediction for aligned RNA sequences. J. Mol. Biol., 319, 1059-1066.
    • (2002) J. Mol. Biol. , vol.319 , pp. 1059-1066
    • Hofacker, I.1
  • 22
    • 70349984002 scopus 로고    scopus 로고
    • Partition function and base pairing probabilities for RNARNA interaction prediction
    • Huang, F.W.D. et al. (2009) Partition function and base pairing probabilities for RNARNA interaction prediction. Bioinformatics, 25, 2646-2654.
    • (2009) Bioinformatics , vol.25 , pp. 2646-2654
    • Huang, F.W.D.1
  • 23
    • 77950472609 scopus 로고    scopus 로고
    • Target prediction and a statistical sampling algorithm for RNARNA interaction
    • Huang, F. et al. (2010) Target prediction and a statistical sampling algorithm for RNARNA interaction. Bioinformatics, 26, 175-181.
    • (2010) Bioinformatics , vol.26 , pp. 175-181
    • Huang, F.1
  • 24
    • 79951538055 scopus 로고    scopus 로고
    • Hfold:RNA pseudoknotted secondary structure prediction using hierarchial folding
    • Giancarlo, R. and Hannenhalli, S. (eds), Springer, Philadephia, PA, USA
    • Jabbari, H. et al. (2007) Hfold:RNA pseudoknotted secondary structure prediction using hierarchial folding. In Giancarlo, R. and Hannenhalli, S. (eds), In Algorithms in Bioinformatics, 7th InternationalWorkshop, WABI 2007. Springer, Philadephia, PA, USA.
    • (2007) Algorithms in Bioinformatics, 7th InternationalWorkshop, WABI 2007
    • Jabbari, H.1
  • 25
    • 0030611726 scopus 로고    scopus 로고
    • Chlamydomonas U2 U4 and U6 snRNAs. An evolutionary conserved putative third interaction between U4 and U6 snrnas which has a counterpart in the U4atac-U6atac snRNA duplex
    • Jakab, G. et al. (1997) Chlamydomonas U2, U4 and U6 snRNAs. An evolutionary conserved putative third interaction between U4 and U6 snrnas which has a counterpart in the U4atac-U6atac snRNA duplex. Biochimie, 79, 387-395.
    • (1997) Biochimie , vol.79 , pp. 387-395
    • Jakab, G.1
  • 26
    • 77956503102 scopus 로고    scopus 로고
    • RactIP: fast and accurate prediction of RNA-RNAinteraction using integer programming
    • Kato, Y. et al. (2010) RactIP: fast and accurate prediction of RNA-RNAinteraction using integer programming. Bioinfomatics, 26, i460-i466.
    • (2010) Bioinfomatics , vol.26
    • Kato, Y.1
  • 27
    • 0034106753 scopus 로고    scopus 로고
    • An unusual structure formed by antisense-target RNA binding involves an extended kissing complex with a four-way junction and a side-by-side helical alignment
    • Kolb, F.A. et al. (2000) An unusual structure formed by antisense-target RNA binding involves an extended kissing complex with a four-way junction and a side-by-side helical alignment. RNA, 6, 311-324.
    • (2000) RNA , vol.6 , pp. 311-324
    • Kolb, F.A.1
  • 28
    • 44349155377 scopus 로고    scopus 로고
    • Computational screen for spliceosomal RNA genes aids in defining the phylogenetic distribution of major and minor spliceosomal components
    • López, M. et al. (2008) Computational screen for spliceosomal RNA genes aids in defining the phylogenetic distribution of major and minor spliceosomal components. Nucleic Acids Res., 36, 3001-3010.
    • (2008) Nucleic Acids Res. , vol.36 , pp. 3001-3010
    • López, M.1
  • 29
    • 33947732940 scopus 로고    scopus 로고
    • A novel family of C. elegans snRNPs contains proteins associated with Trans-splicing
    • MacMorris, M. et al. (2007) A novel family of C. elegans snRNPs contains proteins associated with Trans-splicing. RNA, 13, 511-520.
    • (2007) RNA , vol.13 , pp. 511-520
    • MacMorris, M.1
  • 30
    • 65349106492 scopus 로고    scopus 로고
    • Evolution of spliceosomal snRNA genes in metazoan animals
    • Marz, M. et al. (2008) Evolution of spliceosomal snRNA genes in metazoan animals. J. Mol. Evol., 67, 594-607.
    • (2008) J. Mol. Evol. , vol.67 , pp. 594-607
    • Marz, M.1
  • 31
    • 0033591465 scopus 로고    scopus 로고
    • Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure
    • Mathews, D. 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.1
  • 32
    • 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
  • 33
    • 75449115192 scopus 로고    scopus 로고
    • On the approximation of optimal structures for RNA-RNA interaction
    • Mneimneh, S. (2009) On the approximation of optimal structures for RNA-RNA interaction. IEEE/ACM Trans. Comp. Biol. Bioinf., 6, 682-688.
    • (2009) IEEE/ACM Trans. Comp. Biol. Bioinf. , vol.6 , pp. 682-688
    • Mneimneh, S.1
  • 34
    • 33646877072 scopus 로고    scopus 로고
    • Thermodynamics of RNA-RNA binding
    • Mückstein, U. (2006) Thermodynamics of RNA-RNA binding. Bioinformatics, 22, 1177-1182.
    • (2006) Bioinformatics , vol.22 , pp. 1177-1182
    • Mückstein, U.1
  • 35
    • 84885805331 scopus 로고    scopus 로고
    • Translational control by RNA-RNA interaction: improved computation of RNA-RNA binding thermodynamics
    • Elloumi, M. (eds), of Comm. Comp. Inf. Sci. Springer, Berlin
    • Mückstein, U. et al. (2008) Translational control by RNA-RNA interaction: improved computation of RNA-RNA binding thermodynamics. In Elloumi, M. (eds), BioInformatics Research and Development - BIRD 2008, Vol.13 of Comm. Comp. Inf. Sci. Springer, Berlin, pp. 114-127.
    • (2008) BioInformatics Research and Development - BIRD 2008 , vol.13 , pp. 114-127
    • Mückstein, U.1
  • 36
    • 2342485506 scopus 로고    scopus 로고
    • miRNAs on the move: miRNA biogenesis and the RNAi machinery
    • Murchison, E. and Hannon, G. (2004) miRNAs on the move: miRNA biogenesis and the RNAi machinery. Curr. Opin. Cell. Biol., 16, 223-229.
    • (2004) Curr. Opin. Cell. Biol. , vol.16 , pp. 223-229
    • Murchison, E.1    Hannon, G.2
  • 37
    • 0036184249 scopus 로고    scopus 로고
    • The divergent U12-type splicesome is sequired for pre-mRNA splicing and is essential for development in Drosophila
    • Otake, L. et al. (2002) The divergent U12-type splicesome is sequired for pre-mRNA splicing and is essential for development in Drosophila. Mol. Cell, 9, 439-446.
    • (2002) Mol. Cell. , vol.9 , pp. 439-446
    • Otake, L.1
  • 38
    • 33644667975 scopus 로고    scopus 로고
    • IRIS: Intermolecular RNA interaction search
    • Pervouchine, D. (2004) IRIS: Intermolecular RNA interaction search. Proc. Genome Informatics, 15, 92-101.
    • (2004) Proc. Genome Informatics , vol.15 , pp. 92-101
    • Pervouchine, D.1
  • 39
    • 4644237189 scopus 로고    scopus 로고
    • Fast and effective prediction of microRNA/target duplexes
    • Rehmsmeier, M. et al. (2004) Fast and effective prediction of microRNA/target duplexes. Gene, 10, 1507-1517.
    • (2004) Gene , vol.10 , pp. 1507-1517
    • Rehmsmeier, M.1
  • 40
    • 0038187589 scopus 로고    scopus 로고
    • Small non-coding RNAs, co-ordinators of adaptation processes in Escherichia coli: The RpoS paradigm
    • Repoila, F. et al. (2003) Small non-coding RNAs, co-ordinators of adaptation processes in Escherichia coli: The RpoS paradigm. Mol. Microbiol., 48, 855-861.
    • (2003) Mol. Microbiol. , vol.48 , pp. 855-861
    • Repoila, F.1
  • 41
    • 0033524952 scopus 로고    scopus 로고
    • A dynamic programming algorithms for RNA structure prediction including pseudoknots
    • Rivas, E. and Eddy, S.R. (1999) A dynamic programming algorithms for RNA structure prediction including pseudoknots. J. Mol. Biol., 285, 2053-2068.
    • (1999) J. Mol. Biol. , vol.285 , pp. 2053-2068
    • Rivas, E.1    Eddy, S.R.2
  • 43
    • 56649099274 scopus 로고    scopus 로고
    • Unifying evolutionary and thermodynamic information for RNA folding of multiple alignments
    • Seemann, S. et al. (2008) Unifying evolutionary and thermodynamic information for RNA folding of multiple alignments. Nucleic Acids Res., 36, 6355-6362.
    • (2008) Nucleic Acids Res. , vol.36 , pp. 6355-6362
    • Seemann, S.1
  • 44
    • 78651415661 scopus 로고    scopus 로고
    • PETcofold: Predicting conserved interactions and structures of two multiple alignments of RNA sequences
    • doi:10. 1093/bioinformatics/
    • Seemann, S. et al. (2010a) PETcofold: Predicting conserved interactions and structures of two multiple alignments of RNA sequences. Bioinformatics. doi:10.1093/bioinformatics/btq634.
    • (2010) Bioinformatics
    • Seemann, S.1
  • 45
    • 77952448550 scopus 로고    scopus 로고
    • Hierarchical folding of multiple sequence alignments for the prediction of structures and RNA-RNA interactions
    • Seemann, S. et al. (2010b) Hierarchical folding of multiple sequence alignments for the prediction of structures and RNA-RNA interactions. Algorithms Mol. Biology, 5, 22.
    • (2010) Algorithms Mol. Biology , vol.5 , pp. 22
    • Seemann, S.1
  • 46
    • 0028358644 scopus 로고
    • The spliceosomal U small nuclear RNAs of Ascaris lumbricoides
    • Shambaugh, J. et al. (1994) The spliceosomal U small nuclear RNAs of Ascaris lumbricoides. Mol. Biochem. Parasitol., 64, 349-352.
    • (1994) Mol. Biochem. Parasitol. , vol.64 , pp. 349-352
    • Shambaugh, J.1
  • 47
    • 0036850385 scopus 로고    scopus 로고
    • Domains of human U4atac snRNA required for U12-dependent splicing in vivo
    • Shukla, G. (2002) Domains of human U4atac snRNA required for U12-dependent splicing in vivo. Nucleic Acids Res., 30, 4650-4657.
    • (2002) Nucleic Acids Res. , vol.30 , pp. 4650-4657
    • Shukla, G.1
  • 48
    • 0025344287 scopus 로고
    • The spliceosomal snRNAs of Caenorhabditis elegans
    • Thomas, J. et al. (1990) The spliceosomal snRNAs of Caenorhabditis elegans. Nucleic Acids Res., 18, 2633-2642.
    • (1990) Nucleic Acids Res. , vol.18 , pp. 2633-2642
    • Thomas, J.1
  • 49
    • 0034509631 scopus 로고    scopus 로고
    • Crystal structure of the spliceosomal 15 5kD protein bound to a U4 snRNA fragment
    • Vidovic, I. et al. (2000) Crystal structure of the spliceosomal 15.5kD protein bound to a U4 snRNA fragment. Mol. Cell, 6, 1331-1342.
    • (2000) Mol. Cell. , vol.6 , pp. 1331-1342
    • Vidovic, I.1
  • 50
    • 0036575444 scopus 로고    scopus 로고
    • Antisense RNAs everywhere?
    • Wagner, E.G. and Flärdh, K. (2002) Antisense RNAs everywhere? Trends Genet., 18, 223-226.
    • (2002) Trends Genet , vol.18 , pp. 223-226
    • Wagner, E.G.1    Flärdh, K.2
  • 51
    • 78149355812 scopus 로고    scopus 로고
    • Nupack: analysis and design of nucleic acid systems
    • doi:10.1002/jcc.21596
    • Zadeh, J. et al. (2010) Nupack: analysis and design of nucleic acid systems. J. Comput. Chem., doi:10.1002/jcc.21596.
    • (2010) J. Comput. Chem.
    • Zadeh, J.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.