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Volumn 7, Issue , 2006, Pages

A method for rapid similarity analysis of RNA secondary structures

Author keywords

[No Author keywords available]

Indexed keywords

DYNAMIC PROGRAMMING ALGORITHM; FUNCTION PREDICTION; LEMPEL-ZIV ALGORITHMS; PHYLOGENETIC TREES; RNA SECONDARY STRUCTURES; SECONDARY STRUCTURES; SIMILARITY ANALYSIS; STRUCTURE COMPARISONS;

EID: 33751162430     PISSN: 14712105     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-7-493     Document Type: Article
Times cited : (21)

References (28)
  • 1
    • 0025187499 scopus 로고
    • Comparing multiple RNA secondary structures using tree comparisons
    • Shapiro B, Zhang K: Comparing multiple RNA secondary structures using tree comparisons. Comput Appl Biosci 1990, 6:309-318.
    • (1990) Comput Appl Biosci , vol.6 , pp. 309-318
    • Shapiro, B.1    Zhang, K.2
  • 3
    • 0025264854 scopus 로고
    • The equilibrium partition function and base pair binding probabilities for RNA secondary structure
    • McCaskill JS: The equilibrium partition function and base pair binding probabilities for RNA secondary structure. Biopolymers 1990, 29:1105-1119.
    • (1990) Biopolymers , vol.29 , pp. 1105-1119
    • McCaskill, J.S.1
  • 4
    • 0024386096 scopus 로고
    • Tree graphs of RNA secondary structures and their comparisons
    • Le SY, Nussinov R, Maizel JV: Tree graphs of RNA secondary structures and their comparisons. Comput Biomed Res 1989, 22:461-473.
    • (1989) Comput Biomed Res , vol.22 , pp. 461-473
    • Le, S.Y.1    Nussinov, R.2    Maizel, J.V.3
  • 5
    • 0024061490 scopus 로고
    • An algorithm for comparing multiple RNA secondary structures
    • Shapiro B: An algorithm for comparing multiple RNA secondary structures. Comput Appl Biosci 1988, 4(3):387-393.
    • (1988) Comput Appl Biosci , vol.4 , Issue.3 , pp. 387-393
    • Shapiro, B.1
  • 6
    • 0022146059 scopus 로고
    • Simultaneous solution of the RNA folding, alignment, and protosequence problems
    • Sankoff D: Simultaneous solution of the RNA folding, alignment, and protosequence problems. SIAM J Appl Math 1985, 45:810-825.
    • (1985) SIAM J Appl Math , vol.45 , pp. 810-825
    • Sankoff, D.1
  • 7
    • 0024348264 scopus 로고
    • RNA secondary structures: Comparisons and determination of frequently recurring substructures by consensus
    • Le SY, Owens J, Nussinov R, Chen JH, Shapiro B, Maizel JV: RNA secondary structures: comparisons and determination of frequently recurring substructures by consensus. Comput Appl Biosci 1989, 5:205-210.
    • (1989) Comput Appl Biosci , vol.5 , pp. 205-210
    • Le, S.Y.1    Owens, J.2    Nussinov, R.3    Chen, J.H.4    Shapiro, B.5    Maizel, J.V.6
  • 9
    • 2442647664 scopus 로고    scopus 로고
    • A 3D graphical representation of RNA secondary structure
    • Liao B, Wang TM: A 3D graphical representation of RNA secondary structure. J Biomol Struc Dynamics 2004, 21:827-832.
    • (2004) J Biomol Struc Dynamics , vol.21 , pp. 827-832
    • Liao, B.1    Wang, T.M.2
  • 10
    • 0035324931 scopus 로고    scopus 로고
    • Characterization of DNA primary sequences based on the average distances between bases
    • Randic M, Basak SC: Characterization of DNA primary sequences based on the average distances between bases. J Chem Inf Comput Sci 2001, 41:561-568.
    • (2001) J Chem Inf Comput Sci , vol.41 , pp. 561-568
    • Randic, M.1    Basak, S.C.2
  • 11
    • 18344389019 scopus 로고    scopus 로고
    • Algorithm for coding DNA sequences into "spectrum-like" and "zigzag" representations
    • Zupan J, Randic M: Algorithm for coding DNA sequences into "spectrum-like" and "zigzag" representations. J Chem Inf Comput Sci 2005, 45:309-313.
    • (2005) J Chem Inf Comput Sci , vol.45 , pp. 309-313
    • Zupan, J.1    Randic, M.2
  • 12
    • 0037450561 scopus 로고    scopus 로고
    • Numerical characterization of DNA sequences in a 2-D graphical representation scheme of low degeneracy
    • Guo XF, Nandy A: Numerical characterization of DNA sequences in a 2-D graphical representation scheme of low degeneracy. Chemical Physics Letters 2003, 369:361-366.
    • (2003) Chemical Physics Letters , vol.369 , pp. 361-366
    • Guo, X.F.1    Nandy, A.2
  • 13
    • 0037470662 scopus 로고    scopus 로고
    • Analysis of similarity/dissimilarity of DNA sequences based on novel 2-D graphical representation
    • Randic M, Vracko M, Lers N, Plavsic D: Analysis of similarity/ dissimilarity of DNA sequences based on novel 2-D graphical representation. Chemical Physics Letters 2003, 371:202-207.
    • (2003) Chemical Physics Letters , vol.371 , pp. 202-207
    • Randic, M.1    Vracko, M.2    Lers, N.3    Plavsic, D.4
  • 15
    • 0016880887 scopus 로고
    • On the complexity of finite sequences
    • Lempel A, Ziv J: On the complexity of finite sequences. IEEE T Inform Theory 1976, 22:75-81.
    • (1976) IEEE T Inform Theory , vol.22 , pp. 75-81
    • Lempel, A.1    Ziv, J.2
  • 16
    • 0031841911 scopus 로고    scopus 로고
    • The ribonuclease P database
    • Brown J: The ribonuclease P database. Nucleic Acids Res 1998, 26:351-352.
    • (1998) Nucleic Acids Res , vol.26 , pp. 351-352
    • Brown, J.1
  • 17
    • 0027391688 scopus 로고
    • Secondary structure of RNase MRP RNA as predicted by phylogenetic comparison
    • Schmitt M, Bennett J, Dairaghi D: Secondary structure of RNase MRP RNA as predicted by phylogenetic comparison. FASEB J 1993, 7:208-213.
    • (1993) FASEB J , vol.7 , pp. 208-213
    • Schmitt, M.1    Bennett, J.2    Dairaghi, D.3
  • 19
    • 0000122573 scopus 로고
    • PHYLIP-Phylogeny inference package (version 3.2)
    • Felsenstein J: PHYLIP-Phylogeny inference package (version 3.2). Cladistics 1989, 5:164-166.
    • (1989) Cladistics , vol.5 , pp. 164-166
    • Felsenstein, J.1
  • 20
    • 0030203863 scopus 로고    scopus 로고
    • TREEVIEW: An application to display phylogenetic trees on personal computers
    • Page RDM: TREEVIEW: An application to display phylogenetic trees on personal computers. Computer Applications in the Biosciences 1996, 12:357-358.
    • (1996) Computer Applications in the Biosciences , vol.12 , pp. 357-358
    • Page, R.D.M.1
  • 21
    • 0018369831 scopus 로고
    • Evolutionary change in 5S rRNA secondary structure and a phylogenetic tree of 54 5S rRNA species
    • Hiro H, Osawa S: Evolutionary change in 5S rRNA secondary structure and a phylogenetic tree of 54 5S rRNA species. Proc Natl Acad Sci USA 1979, 76:381-385.
    • (1979) Proc Natl Acad Sci USA , vol.76 , pp. 381-385
    • Hiro, H.1    Osawa, S.2
  • 22
    • 0022516669 scopus 로고
    • Evolutionary change in 5S rRNA secondary structure and a phylogenetic tree of 352 5S rRNA species
    • Hiro H, Osawa S: Evolutionary change in 5S rRNA secondary structure and a phylogenetic tree of 352 5S rRNA species. Proc Natl Acad Sci USA 1986, 19:163-172.
    • (1986) Proc Natl Acad Sci USA , vol.19 , pp. 163-172
    • Hiro, H.1    Osawa, S.2
  • 23
    • 0028983910 scopus 로고
    • Birth of the snoRNPs: The evolution of RNase MRP and the eukaryotic pre-rRNA-processing system
    • Morrissey JP, Tollervey D: Birth of the snoRNPs: the evolution of RNase MRP and the eukaryotic pre-rRNA-processing system. TIBS 1995, 20:78-82.
    • (1995) TIBS , vol.20 , pp. 78-82
    • Morrissey, J.P.1    Tollervey, D.2
  • 24
    • 0029868741 scopus 로고    scopus 로고
    • Structural and functional similarities between MRP and RNase P
    • Reddy R, Shimba S: Structural and functional similarities between MRP and RNase P. Mol Biol Rep 1996, 22:81-85.
    • (1996) Mol Biol Rep , vol.22 , pp. 81-85
    • Reddy, R.1    Shimba, S.2
  • 26
    • 0033814944 scopus 로고    scopus 로고
    • Use of RNA secondary structure for studying the evolution of RNase P and RNase MRP
    • Collins LJ, Moulton V, Penny D: Use of RNA secondary structure for studying the evolution of RNase P and RNase MRP. J Mol Evol 2000, 51:194-204.
    • (2000) J Mol Evol , vol.51 , pp. 194-204
    • Collins, L.J.1    Moulton, V.2    Penny, D.3
  • 27
    • 4644345118 scopus 로고    scopus 로고
    • Pure Multiple RNA Secondary Structure Alignments: A Progressive Profile Approach
    • Höchsmann M, Voss B, Giegerich R: Pure Multiple RNA Secondary Structure Alignments: A Progressive Profile Approach. IEEE ICBB 2004, 1:53-62.
    • (2004) IEEE ICBB , vol.1 , pp. 53-62
    • Höchsmann, M.1    Voss, B.2    Giegerich, R.3
  • 28
    • 0242643741 scopus 로고    scopus 로고
    • A new sequence distance measure for phylogenetic tree construction
    • Otu HH, Sayood K: A new sequence distance measure for phylogenetic tree construction. Bioinformatics 2003, 19:2122-2130.
    • (2003) Bioinformatics , vol.19 , pp. 2122-2130
    • Otu, H.H.1    Sayood, K.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.