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Volumn 5577 LNCS, Issue , 2009, Pages 249-262

Sparse RNA folding: Time and space efficient algorithms

Author keywords

[No Author keywords available]

Indexed keywords

BASE-PAIRING; CARDINALITIES; CLASSICAL ALGORITHMS; INPUT SEQUENCE; RNA FOLDING; SECONDARY STRUCTURES; SIMULTANEOUS ALIGNMENT; SPACE ALGORITHMS; SPACE COMPLEXITY; SPACE REDUCTIONS; SPEED-UPS; SUB-PROBLEMS; SUPPORTING MATERIAL; TIME AND SPACE;

EID: 70350639137     PISSN: 03029743     EISSN: 16113349     Source Type: Book Series    
DOI: 10.1007/978-3-642-02441-2_22     Document Type: Conference Paper
Times cited : (23)

References (21)
  • 1
    • 33847183553 scopus 로고    scopus 로고
    • Consortium, A.F.B., Backofen, R., Bernhart, S.H., Flamm, C., Fried, C., Fritzsch, G., Hackermuller, J., Hertel, J., Hofacker, I.L., Missal, K., Mosig, A., Prohaska, S.J., Rose, D., Stadler, P.F., Tanzer, A., Washietl, S., Will, S.: RNAs everywhere: genome-wide annotation of structured RNAs. Journal of Experimental Zoology Part B: Molecular and Developmental Evolution 308(1), 1-25 (2007)
    • Consortium, A.F.B., Backofen, R., Bernhart, S.H., Flamm, C., Fried, C., Fritzsch, G., Hackermuller, J., Hertel, J., Hofacker, I.L., Missal, K., Mosig, A., Prohaska, S.J., Rose, D., Stadler, P.F., Tanzer, A., Washietl, S., Will, S.: RNAs everywhere: genome-wide annotation of structured RNAs. Journal of Experimental Zoology Part B: Molecular and Developmental Evolution 308(1), 1-25 (2007)
  • 2
    • 0042121256 scopus 로고    scopus 로고
    • Mfold web server for nucleic acid folding and hybridization prediction
    • Zuker, M.: Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Research (13), 3406-3415 (2003)
    • (2003) Nucleic Acids Research , vol.13 , pp. 3406-3415
    • Zuker, M.1
  • 3
    • 0043123153 scopus 로고    scopus 로고
    • Vienna RNA secondary structure server
    • Hofacker, I.L.: Vienna RNA secondary structure server. Nucleic Acids Research (13), 3429-3431 (2003)
    • (2003) Nucleic Acids Research , vol.13 , pp. 3429-3431
    • Hofacker, I.L.1
  • 4
    • 0024806949 scopus 로고
    • Computer prediction of RNA structure
    • Zuker, M.: Computer prediction of RNA structure. Methods Enzymol. 180, 262-288 (1989)
    • (1989) Methods Enzymol , vol.180 , pp. 262-288
    • Zuker, M.1
  • 6
    • 0018254569 scopus 로고
    • RNA secondary structure: A complete mathematical analysis
    • Waterman, M., Smith, T.: RNA secondary structure: a complete mathematical analysis. Mathematical Biosciences 42, 257-266 (1978)
    • (1978) Mathematical Biosciences , vol.42 , pp. 257-266
    • Waterman, M.1    Smith, T.2
  • 7
    • 0019082587 scopus 로고
    • Fast algorithm for predicting the secondary structure of single-stranded RNA
    • Nussinov, R., Jacobson, A.B.: Fast algorithm for predicting the secondary structure of single-stranded RNA. PNAS 77(11), 6309-6313 (1980)
    • (1980) PNAS , vol.77 , Issue.11 , pp. 6309-6313
    • Nussinov, R.1    Jacobson, A.B.2
  • 8
    • 0019876473 scopus 로고
    • Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information
    • Zuker, M., Stiegler, P.: Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information. Nucleic Acids Research 9(1), 133-148 (1981)
    • (1981) Nucleic Acids Research , vol.9 , Issue.1 , pp. 133-148
    • Zuker, M.1    Stiegler, P.2
  • 9
    • 0042545055 scopus 로고    scopus 로고
    • Approximation and exact algorithms for RNA secondary structure prediction and recognition of stochastic context-free languages
    • Akutsu, T.: Approximation and exact algorithms for RNA secondary structure prediction and recognition of stochastic context-free languages. Journal of Combinatorial Optimization 3, 321-336 (1999)
    • (1999) Journal of Combinatorial Optimization , vol.3 , pp. 321-336
    • Akutsu, T.1
  • 11
    • 35448979108 scopus 로고    scopus 로고
    • More algorithms for all-pairs shortest paths in weighted graphs
    • STOC, pp
    • Chan, T.M.: More algorithms for all-pairs shortest paths in weighted graphs. In: Proc. 39th Symposium on the Theory of Computing (STOC), pp. 590-598 (2007)
    • (2007) Proc. 39th Symposium on the Theory of Computing , pp. 590-598
    • Chan, T.M.1
  • 12
    • 0022146059 scopus 로고
    • Simultaneous solution of the RNA folding, alignment and protose-quence problems
    • Sankoff, D.: Simultaneous solution of the RNA folding, alignment and protose-quence problems. SIAM Journal on Applied Mathematics 45(5), 810-825 (1985)
    • (1985) SIAM Journal on Applied Mathematics , vol.45 , Issue.5 , pp. 810-825
    • Sankoff, D.1
  • 13
    • 0036295198 scopus 로고    scopus 로고
    • Dynalign: An algorithm for finding the secondary structure common to two RNA sequences
    • Mathews, D.H., Turner, D.H.: Dynalign: an algorithm for finding the secondary structure common to two RNA sequences. Journal of Molecular Biology 317(2), 191-203 (2002)
    • (2002) Journal of Molecular Biology , vol.317 , Issue.2 , pp. 191-203
    • Mathews, D.H.1    Turner, D.H.2
  • 14
    • 16344363338 scopus 로고
    • Pairwise local structural alignment of RNA sequences with sequence similarity less than 40%
    • 2005
    • Havgaard, J., Lyngso, R., Stormo, G., Gorodkin, J.: Pairwise local structural alignment of RNA sequences with sequence similarity less than 40%. Bioinfor-matics 21(9), 1815-1824 (2005)
    • (1815) Bioinfor-matics , vol.21 , Issue.9
    • Havgaard, J.1    Lyngso, R.2    Stormo, G.3    Gorodkin, J.4
  • 16
    • 34247598415 scopus 로고    scopus 로고
    • Inferring non-coding RNA families and classes by means of genome-scale structure-based clustering
    • Will, S., Reiche, K., Hofacker, I.L., Stadler, P.F., Backofen, R.: Inferring non-coding RNA families and classes by means of genome-scale structure-based clustering. PLOS Computational Biology 3(4), e65 (2007)
    • (2007) PLOS Computational Biology , vol.3 , Issue.4
    • Will, S.1    Reiche, K.2    Hofacker, I.L.3    Stadler, P.F.4    Backofen, R.5
  • 17
    • 13344262673 scopus 로고    scopus 로고
    • A comprehensive comparison of comparative RNA structure prediction approaches
    • Gardner, P.P., Giegerich, R.: A comprehensive comparison of comparative RNA structure prediction approaches. BMC Bioinformatics 5, 140 (2004)
    • (2004) BMC Bioinformatics , vol.5 , pp. 140
    • Gardner, P.P.1    Giegerich, R.2
  • 18
    • 33748527840 scopus 로고    scopus 로고
    • A faster and more space-efficient algorithm for inferring arc-annotations of RNA sequences through alignment
    • Jansson, J., Ng, S.K., Sung, W.K., Willy, H.: A faster and more space-efficient algorithm for inferring arc-annotations of RNA sequences through alignment. Al-gorithmica 46(2), 223-245 (2006)
    • (2006) Al-gorithmica , vol.46 , Issue.2 , pp. 223-245
    • Jansson, J.1    Ng, S.K.2    Sung, W.K.3    Willy, H.4
  • 20
    • 0016518550 scopus 로고
    • A linear space algorithm for computing maximal common subsequences
    • Hirschberg, D.S.: A linear space algorithm for computing maximal common subsequences. Communications of the ACM 18(6), 341-343 (1975)
    • (1975) Communications of the ACM , vol.18 , Issue.6 , pp. 341-343
    • Hirschberg, D.S.1
  • 21
    • 84976825385 scopus 로고
    • Algorithms for the longest common subsequence problem
    • Hirschberg, D.S.: Algorithms for the longest common subsequence problem. JACM 24, 664-675 (1977)
    • (1977) JACM , vol.24 , pp. 664-675
    • Hirschberg, D.S.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.