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Volumn 6, Issue 2, 2008, Pages 192-204

Shuffling biological sequences with motif constraints

Author keywords

Motifs constraints; NP completeness; Random sequence generation

Indexed keywords

CONSTRAINT THEORY; DECISION MAKING; INTEGER PROGRAMMING; LEARNING ALGORITHMS; SET THEORY; THEOREM PROVING;

EID: 42249099020     PISSN: 15708667     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jda.2007.06.001     Document Type: Article
Times cited : (14)

References (21)
  • 2
    • 0000052835 scopus 로고
    • A random walk construction of uniform spanning trees and uniform labelled trees
    • Aldous D. A random walk construction of uniform spanning trees and uniform labelled trees. SIAM J. Discrete Math. 3 (1990) 450-465
    • (1990) SIAM J. Discrete Math. , vol.3 , pp. 450-465
    • Aldous, D.1
  • 3
    • 0022360113 scopus 로고
    • Significance of nucleotide sequence alignments: A method for random sequence permutation that preserves dinucleotide and codon usage
    • Altschul S., and Erickson B. Significance of nucleotide sequence alignments: A method for random sequence permutation that preserves dinucleotide and codon usage. Mol. Biol. Evol. 2 (1985) 526-538
    • (1985) Mol. Biol. Evol. , vol.2 , pp. 526-538
    • Altschul, S.1    Erickson, B.2
  • 5
    • 84987013936 scopus 로고
    • On graphs with polynomially solvable maximum-weight clique problem
    • Balas E., and Yu C. On graphs with polynomially solvable maximum-weight clique problem. Networks 19 (1989) 247-253
    • (1989) Networks , vol.19 , pp. 247-253
    • Balas, E.1    Yu, C.2
  • 6
    • 0033858202 scopus 로고    scopus 로고
    • Patterns of variant polyadenylation signal usage in human genes
    • Beaudoing E., Freier S., Wyatt J., Claverie J., and Gautheret D. Patterns of variant polyadenylation signal usage in human genes. Genome Res. 10 (2000) 1001-1010
    • (2000) Genome Res. , vol.10 , pp. 1001-1010
    • Beaudoing, E.1    Freier, S.2    Wyatt, J.3    Claverie, J.4    Gautheret, D.5
  • 8
    • 84959049129 scopus 로고    scopus 로고
    • Assessing statistical significance on overrepresented oligonucleotides
    • Proceedings of WABI'01. Gascuel O., and Moret B. (Eds), Springer
    • Denise A., Régnier M., and Vandenbogaert M. Assessing statistical significance on overrepresented oligonucleotides. In: Gascuel O., and Moret B. (Eds). Proceedings of WABI'01. Lecture Notes in Computer Science vol. 2149 (2001), Springer 85-97
    • (2001) Lecture Notes in Computer Science , vol.2149 , pp. 85-97
    • Denise, A.1    Régnier, M.2    Vandenbogaert, M.3
  • 9
    • 0020680218 scopus 로고
    • Random sequences
    • Fitch W. Random sequences. J. Mol. Biol. 163 (1983) 171-176
    • (1983) J. Mol. Biol. , vol.163 , pp. 171-176
    • Fitch, W.1
  • 13
    • 0021760111 scopus 로고
    • On the statistical significance of nucleic acid similarities
    • Lipman D., Wilbur W., Smith T., and Waterman M. On the statistical significance of nucleic acid similarities. Nucleic Acids Res. 12 (1984) 215-226
    • (1984) Nucleic Acids Res. , vol.12 , pp. 215-226
    • Lipman, D.1    Wilbur, W.2    Smith, T.3    Waterman, M.4
  • 15
    • 0000162904 scopus 로고    scopus 로고
    • How to get a perfectly random sample from a generic Markov chain and generate a random spanning tree of a directed graph
    • Propp J., and Wilson D. How to get a perfectly random sample from a generic Markov chain and generate a random spanning tree of a directed graph. J. Algorithms 27 (1998) 170-217
    • (1998) J. Algorithms , vol.27 , pp. 170-217
    • Propp, J.1    Wilson, D.2
  • 16
    • 0000794292 scopus 로고    scopus 로고
    • A unified approach to word occurrence probabilities
    • Régnier M. A unified approach to word occurrence probabilities. Discrete Appl. Math. 104 (2000) 259-280
    • (2000) Discrete Appl. Math. , vol.104 , pp. 259-280
    • Régnier, M.1
  • 17
    • 0034125366 scopus 로고    scopus 로고
    • Probabilistic and statistical properties of words: An overview
    • Reinert G., Schbath S., and Waterman M. Probabilistic and statistical properties of words: An overview. J. Comput. Biol. 7 (2000) 1-46
    • (2000) J. Comput. Biol. , vol.7 , pp. 1-46
    • Reinert, G.1    Schbath, S.2    Waterman, M.3
  • 18
    • 1342309208 scopus 로고    scopus 로고
    • Metrics for comparing regulatory sequences on the basis of pattern counts
    • van Helden J. Metrics for comparing regulatory sequences on the basis of pattern counts. Bioinformatics 20 (2004) 399-406
    • (2004) Bioinformatics , vol.20 , pp. 399-406
    • van Helden, J.1
  • 19
    • 0032483307 scopus 로고    scopus 로고
    • Extracting regulatory sites from the upstream region of yeast genes by computational analysis of oligonucleotide frequencies
    • van Helden J., André B., and Collado-Vides J. Extracting regulatory sites from the upstream region of yeast genes by computational analysis of oligonucleotide frequencies. J. Mol. Biol. 281 (1998) 827-842
    • (1998) J. Mol. Biol. , vol.281 , pp. 827-842
    • van Helden, J.1    André, B.2    Collado-Vides, J.3
  • 20
    • 0033379116 scopus 로고    scopus 로고
    • Promoter sequences and algorithmical methods for identifying them
    • Vanet A., Marsan L., and Sagot M.-F. Promoter sequences and algorithmical methods for identifying them. Res. Microbiol. 150 (1999) 779-799
    • (1999) Res. Microbiol. , vol.150 , pp. 779-799
    • Vanet, A.1    Marsan, L.2    Sagot, M.-F.3
  • 21
    • 0029711422 scopus 로고    scopus 로고
    • D. Wilson, Generating random spanning trees more quickly than the cover time, in: Proceedings of the Twenty-Eighth Annual ACM Symposium on the Theory of Computing, 1996, pp. 296-303
    • D. Wilson, Generating random spanning trees more quickly than the cover time, in: Proceedings of the Twenty-Eighth Annual ACM Symposium on the Theory of Computing, 1996, pp. 296-303


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.