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Volumn 27, Issue 14, 2011, Pages 1934-1940

Fast accessibility-based prediction of RNA-RNA interactions

Author keywords

[No Author keywords available]

Indexed keywords

RNA;

EID: 79959933227     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btr281     Document Type: Article
Times cited : (45)

References (40)
  • 1
    • 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
  • 2
    • 0042622372 scopus 로고    scopus 로고
    • RNAsoft: a suite of RNA secondary structure prediction and design software tools
    • Andronescu,M.et al. (2003) RNAsoft: a suite of RNA secondary structure prediction and design software tools. Nucleic Acids Res., 31, 3416-3422.
    • (2003) Nucleic Acids Res , vol.31 , pp. 3416-3422
    • Andronescu, M.1
  • 3
    • 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 omplex. J. Mol. Biol., 300, 1101-1112.
    • (2000) J. Mol. Biol. , vol.300 , pp. 1101-1112
    • Argaman, L.1    Altuvia, S.2
  • 4
    • 0036703184 scopus 로고    scopus 로고
    • The expanding snoRNA world
    • Bachellerie,J.et al. (2002) The expanding snoRNA world. Biochimie, 84, 775-790.
    • (2002) Biochimie , vol.84 , pp. 775-790
    • Bachellerie, J.1
  • 5
    • 33847183553 scopus 로고    scopus 로고
    • RNAs everywhere: genome-wide annotation of structured RNAs
    • The Athanasius F. Bompfünewerer RNA Consortium
    • Backofen,R.et al.; The Athanasius F. Bompfünewerer RNA Consortium (2007). RNAs everywhere: genome-wide annotation of structured RNAs. J. xp. Zool. BMol. Dev. Evol., 308B, 1-25.
    • (2007) J. Exp. Zool. BMol. Dev. Evol. , vol.308 B , pp. 1-25
    • Backofen, R.1
  • 6
    • 0036008547 scopus 로고    scopus 로고
    • Control of developmental timing by small temporal RNAs: a paradigm for RNA-mediated regulation of gene expression
    • Banerjee,D. and Slack,F. (2002) Control of developmental timing by small temporal RNAs: a paradigm for RNA-mediated regulation of gene expression. Bioessays, 24, 119-129.
    • (2002) Bioessays , vol.24 , pp. 119-129
    • Banerjee, D.1    Slack, F.2
  • 7
    • 0026919885 scopus 로고
    • RNA editing in trypanosomes. the us(e) of guide RNAs
    • Benne,R. (1992) RNA editing in trypanosomes. the us(e) of guide RNAs. Mol. Biol. Rep., 16, 217-227.
    • (1992) Mol. Biol. Rep. , vol.16 , pp. 217-227
    • Benne, R.1
  • 8
    • 33644853766 scopus 로고    scopus 로고
    • Local RNA base pairing probabilities in large sequences
    • Bernhart,S.et al. (2006a) Local RNA base pairing probabilities in large sequences. Bioinformatics, 22, 614-615.
    • (2006) Bioinformatics , vol.22 , pp. 614-615
    • Bernhart, S.1
  • 9
    • 33744979613 scopus 로고    scopus 로고
    • Partition function and base pairing probabilities of RNA heterodimers
    • Bernhart,S.et al. (2006b) 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
  • 10
    • 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.
    • (2008) BMC Bioinformatics , vol.9 , pp. 474
    • Bernhart, S.1
  • 11
    • 36448958364 scopus 로고    scopus 로고
    • Variations on RNAfolding and alignment: lessons from benasque
    • Bompfünewerer,A.et al. (2008)Variations on RNAfolding and alignment: lessons from benasque. J. Math. Biol., 56, 129-144.
    • (2008) J. Math. Biol. , vol.56 , pp. 129-144
    • Bompfünewerer, A.1
  • 12
    • 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, 4, 2849-2856.
    • (2008) Bioinformatics , vol.24 , pp. 2849-2856
    • Busch, A.1
  • 13
    • 34248229182 scopus 로고    scopus 로고
    • Exploration of pairing constraints identifies a 9 base-pair core within box c/d snoRNA-rRNA duplexes
    • Chen,C. et al, (2007) Exploration of pairing constraints identifies a 9 base-pair core within box c/d snoRNA-rRNA duplexes. J. Mol. Biol., 369, 771-83.
    • (2007) J. Mol. Biol. , vol.369 , pp. 771-783
    • Chen, C.1
  • 14
    • 79960110354 scopus 로고    scopus 로고
    • of Lecture Notes in Computer Science. Springer, Berlin, Heidelberg
    • Chitsaz,H.et al. (2009) Algorithms in Bioinformatics, Vol. 5724 of Lecture Notes in Computer Science. Springer, Berlin, Heidelberg.
    • (2009) Algorithms in Bioinformatics , vol.5724
    • Chitsaz, H.1
  • 15
    • 67349095027 scopus 로고    scopus 로고
    • Small RNA-induced differential degradation of the polycistronic mRNA iscrsua
    • Desnoyers,G.et al. (2009) Small RNA-induced differential degradation of the polycistronic mRNA iscrsua. EMBO J., 28, 1551-1561.
    • (2009) EMBO J. , vol.28 , pp. 1551-1561
    • Desnoyers, G.1
  • 16
    • 3042735602 scopus 로고    scopus 로고
    • Prediction of hybridization and melting for doublestranded nucleic acids
    • Dimitrov,R. and Zuker,M. (2004) Prediction of hybridization and melting for doublestranded nucleic acids. Biophys. J., 87, 215-226.
    • (2004) Biophys. J. , vol.87 , pp. 215-226
    • Dimitrov, R.1    Zuker, M.2
  • 17
    • 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
  • 18
    • 3042666256 scopus 로고    scopus 로고
    • Muscle: multiple sequence alignment with high accuracy and high throughput
    • Edgar,R. (2004) Muscle: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res., 32, 1792-1797.
    • (2004) Nucleic Acids Res. , vol.32 , pp. 1792-1797
    • Edgar, R.1
  • 19
    • 0025069836 scopus 로고
    • Complex formed by complementary RNA stemloops and its stabilization by a protein: function of coie1 rom protein
    • Eguchi,Y. and Tomizawa,J. (1990) Complex formed by complementary RNA stemloops and its stabilization by a protein: function of coie1 rom protein. ell, 60, 199-209.
    • (1990) Cell , vol.60 , pp. 199-209
    • Eguchi, Y.1    Tomizawa, J.2
  • 20
    • 0032545933 scopus 로고    scopus 로고
    • Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans
    • Fire,A.et al. (1998) Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans. Nature, 391, 806-811.
    • (1998) Nature , vol.391 , pp. 806-811
    • Fire, A.1
  • 21
    • 58149191274 scopus 로고    scopus 로고
    • Rfam: updates to the RNA families database
    • Gardner,P.et al. (2009) Rfam: updates to the RNA families database. Nucleic Acids Res., 37, 136-140.
    • (2009) Nucleic Acids Res. , vol.37 , pp. 136-140
    • Gardner, P.1
  • 22
    • 34249772381 scopus 로고
    • Fast folding and comparison of RNA secondary structures
    • Hofacker,I.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.1
  • 23
    • 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
  • 24
    • 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
  • 25
    • 33846340147 scopus 로고    scopus 로고
    • An RNA transcriptional regulator templates its own regulatory RNA
    • Kugel,J. and Goodrich,J. (2007) An RNA transcriptional regulator templates its own regulatory RNA. Nat. Chem. Biol., 3, 89-90.
    • (2007) Nat. Chem. Biol. , vol.3 , pp. 89-90
    • Kugel, J.1    Goodrich, J.2
  • 26
    • 36448991500 scopus 로고    scopus 로고
    • Clustal W and Clustal X version 2.0
    • Larkin,M.et al. (2007) Clustal W and Clustal X version 2.0. Bioinformatics, 23, 2947-2948.
    • (2007) Bioinformatics , vol.23 , pp. 2947-2948
    • Larkin, M.1
  • 27
    • 0037007078 scopus 로고    scopus 로고
    • A small RNA regulates the expression of genes involved in iron metabolism in Escherichia coli
    • Massé,E. and Gottesman,S. (2002) A small RNA regulates the expression of genes involved in iron metabolism in Escherichia coli. Proc. Natl Acad. ci. USA, 99, 4620-4625.
    • (2002) Proc. Natl Acad. Sci. USA , vol.99 , pp. 4620-4625
    • Massé, E.1    Gottesman, S.2
  • 28
    • 33646877072 scopus 로고    scopus 로고
    • Thermodynamics of RNA-RNA binding
    • Mückstein,U.et al. (2006) Thermodynamics of RNA-RNA binding. Bioinformatics, 22, 1177-1182.
    • (2006) Bioinformatics , vol.22 , pp. 1177-1182
    • Mückstein, U.1
  • 29
    • 84885805331 scopus 로고    scopus 로고
    • Translational Control by RNA-RNA Interaction: Improved Computation of RNA-RNA Binding Thermodynamics
    • Elloumi,M. et al. (eds) Springer, Berlin/Heidelberg
    • Mückstein,U.et al. (2008) Translational Control by RNA-RNA Interaction: Improved Computation of RNA-RNA Binding Thermodynamics. In Elloumi,M. et al. (eds) Bioinformatics Research and Development, Vol. 13, Springer, Berlin/Heidelberg, pp. 114-127.
    • (2008) Bioinformatics Research and Development , vol.13 , pp. 114-127
    • Mückstein, U.1
  • 30
    • 33644667975 scopus 로고    scopus 로고
    • Iris: intermolecular rna interaction search
    • Pervouchine,D. (2004) Iris: intermolecular rna interaction search. Genome Inform., 15, 92-101.
    • (2004) Genome Inform , vol.15 , pp. 92-101
    • Pervouchine, D.1
  • 31
    • 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. RNA, 10, 1507-1517.
    • (2004) RNA , vol.10 , pp. 1507-1517
    • Rehmsmeier, M.1
  • 32
    • 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, 6355-362.
    • (2008) Nucleic Acids Res. , vol.36 , pp. 6355-6362
    • Seemann, S.1
  • 33
    • 77952448550 scopus 로고    scopus 로고
    • Hierarchical folding of multiple sequence alignments for the prediction of structures and RNA-RNA interactions
    • Seemann,S.et al. (2010) Hierarchical folding of multiple sequence alignments for the prediction of structures and RNA-RNA interactions. Algorithms ol. Biol., 5, 22.
    • (2010) Algorithms Mol. Biol. , vol.5 , pp. 22
    • Seemann, S.1
  • 34
    • 78651415661 scopus 로고    scopus 로고
    • PETcofold: predicting conserved interactions and structures of two multiple alignments of RNA sequences
    • Seemann,S.E.et al. (2011) PETcofold: predicting conserved interactions and structures of two multiple alignments of RNA sequences. Bioinformatics, 7, 211-219.
    • (2011) Bioinformatics , vol.27 , pp. 211-219
    • Seemann, S.E.1
  • 35
    • 34748871477 scopus 로고    scopus 로고
    • Regulation of gene expression by small non-coding RNAs: a quantitative view
    • Shimoni,Y.et al. (2007) Regulation of gene expression by small non-coding RNAs: a quantitative view. Mol. Syst. Biol., 3, 138.
    • (2007) Mol. Syst. Biol. , vol.3 , pp. 138
    • Shimoni, Y.1
  • 36
    • 33845713571 scopus 로고    scopus 로고
    • The RNA chaperone hfq is essential for the virulence of Salmonella typhirium
    • Sittka,A.et al. (2007) The RNA chaperone hfq is essential for the virulence of Salmonella typhirium. Mol. Microbiol., 63, 193-217.
    • (2007) Mol. Microbiol. , vol.63 , pp. 193-217
    • Sittka, A.1
  • 37
    • 4243170045 scopus 로고    scopus 로고
    • Identification of Drosophila MicroRNA targets
    • Stark,A.et al. (2003) Identification of Drosophila MicroRNA targets. PLoS Biol., 1, e60.
    • (2003) PLoS Biol. , vol.1
    • Stark, A.1
  • 38
    • 55749083578 scopus 로고    scopus 로고
    • Rnaplex: a fast tool for RNA-RNA interaction search
    • Tafer,H. and Hofacker,I. (2008) Rnaplex: a fast tool for RNA-RNA interaction search. Bioinformatics, 24, 2657-2663.
    • (2008) Bioinformatics , vol.24 , pp. 2657-2663
    • Tafer, H.1    Hofacker, I.2
  • 39
    • 34748842534 scopus 로고    scopus 로고
    • A conserved small RNA promotes discoordinate expression of the glmUS operon mRNA to activate GlmS synthesis
    • Urban,J.et al. (2007) A conserved small RNA promotes discoordinate expression of the glmUS operon mRNA to activate GlmS synthesis. J. Mol. Biol., 373, 521-528.
    • (2007) J. Mol. Biol. , vol.373 , pp. 521-528
    • Urban, J.1
  • 40
    • 0030614546 scopus 로고    scopus 로고
    • Cloning of caenorhabditis u2af65: an alternatively spliced RNA containing a novel exon
    • Zorio,D.et al. (1997) Cloning of caenorhabditis u2af65: an alternatively spliced RNA containing a novel exon. Mol. Cell Biol., 17, 946-953.
    • (1997) Mol. Cell Biol. , vol.17 , pp. 946-953
    • Zorio, D.1


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