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Volumn 4023 LNBI, Issue , 2007, Pages 198-211

Improved pattern-driven algorithms for motif finding in DNA sequences

Author keywords

[No Author keywords available]

Indexed keywords

BINDING SITES; DNA SEQUENCES; GENES; PROBLEM SOLVING;

EID: 34547446139     PISSN: 03029743     EISSN: 16113349     Source Type: Conference Proceeding    
DOI: None     Document Type: Conference Paper
Times cited : (17)

References (37)
  • 1
    • 1842503722 scopus 로고    scopus 로고
    • Incremental paradigms of motif discovery
    • Apostolico, A., Parida, L.: Incremental paradigms of motif discovery. J. Comp. Biol. 11 (2004) 15-25
    • (2004) J. Comp. Biol , vol.11 , pp. 15-25
    • Apostolico, A.1    Parida, L.2
  • 3
    • 0038716277 scopus 로고    scopus 로고
    • Barash, Y., Elidan, G., Friedman, N., Kaplan, T.: Modeling dependencies in protein-DNA binding sites. Proc. 7th Ann. Int. Conf. Res. Comp. Mol. Biol. (RE-COMB'2003) 28-37
    • Barash, Y., Elidan, G., Friedman, N., Kaplan, T.: Modeling dependencies in protein-DNA binding sites. Proc. 7th Ann. Int. Conf. Res. Comp. Mol. Biol. (RE-COMB'2003) 28-37
  • 5
    • 0036110853 scopus 로고    scopus 로고
    • Finding motifs using random projections
    • Buhler, J., Tompa, M.: Finding motifs using random projections. J. Comp. Biol. 9 (2002) 225-242
    • (2002) J. Comp. Biol , vol.9 , pp. 225-242
    • Buhler, J.1    Tompa, M.2
  • 6
    • 2442591721 scopus 로고    scopus 로고
    • Eskin, E.: From profiles to patterns and back again: a branch and bound algorithm for finding near optimal motif profiles. Proc. 8th Ann. Int. Conf. Res. Comp. Mol. Biol. (RECOMB'2004) 115-124
    • Eskin, E.: From profiles to patterns and back again: a branch and bound algorithm for finding near optimal motif profiles. Proc. 8th Ann. Int. Conf. Res. Comp. Mol. Biol. (RECOMB'2004) 115-124
  • 7
    • 0344376570 scopus 로고    scopus 로고
    • Finding composite regulatory patterns in DNA sequences
    • Eskin, E., Pevzner, P.A.: Finding composite regulatory patterns in DNA sequences. Bioinformatics 18 (2002) S354-363
    • (2002) Bioinformatics , vol.18
    • Eskin, E.1    Pevzner, P.A.2
  • 8
    • 19544379737 scopus 로고    scopus 로고
    • A Gibbs sampler for identification of symmetrically structured, spaced DNA motifs with improved estimation of the signal length
    • Favorov, A.V., Gelfand, M.S., Gerasimova, A.V., Ravcheev, D.A., Mironov, A.A., Makeev, V.J.: A Gibbs sampler for identification of symmetrically structured, spaced DNA motifs with improved estimation of the signal length. Bioinformatics 21 (2005) 2240-2245
    • (2005) Bioinformatics , vol.21 , pp. 2240-2245
    • Favorov, A.V.1    Gelfand, M.S.2    Gerasimova, A.V.3    Ravcheev, D.A.4    Mironov, A.A.5    Makeev, V.J.6
  • 9
    • 0029146491 scopus 로고
    • Identification of common motifs in unaligned DNA sequences: Application to Escherichia coli Lrp regulon
    • Fraenkel, Y.M., Mandel, Y., Friedberg, D., Margalit, H.: Identification of common motifs in unaligned DNA sequences: application to Escherichia coli Lrp regulon. Comp. Appl. Biosci. 11 (1995) 379-387
    • (1995) Comp. Appl. Biosci , vol.11 , pp. 379-387
    • Fraenkel, Y.M.1    Mandel, Y.2    Friedberg, D.3    Margalit, H.4
  • 10
    • 0022358896 scopus 로고
    • Rigorous pattern-recognition methods for DNA sequences. Analysis of promoter sequences from Escherichia coli
    • Galas, D.J., Eggert, M., Waterman, M.S.: Rigorous pattern-recognition methods for DNA sequences. Analysis of promoter sequences from Escherichia coli. J. Mol. Biol. 186 (1985) 117-128
    • (1985) J. Mol. Biol , vol.186 , pp. 117-128
    • Galas, D.J.1    Eggert, M.2    Waterman, M.S.3
  • 11
    • 0034894539 scopus 로고    scopus 로고
    • Identifying target sites for cooperatively binding factors
    • GuhaThakurta, D., Stormo, G.D.: Identifying target sites for cooperatively binding factors. Bioinformatics 17 (2001) 608-621
    • (2001) Bioinformatics , vol.17 , pp. 608-621
    • GuhaThakurta, D.1    Stormo, G.D.2
  • 12
    • 0034628901 scopus 로고    scopus 로고
    • Computational identification of cis-regulatory elements associated with groups of functionally related genes in Saccharomyces cerevisiae
    • Hughes, J.D., Estep, P.W., Tavazoie, S., Church, G.M.: Computational identification of cis-regulatory elements associated with groups of functionally related genes in Saccharomyces cerevisiae. J. Mol. Biol. 296 (2000) 1205-1214
    • (2000) J. Mol. Biol , vol.296 , pp. 1205-1214
    • Hughes, J.D.1    Estep, P.W.2    Tavazoie, S.3    Church, G.M.4
  • 13
    • 0036772332 scopus 로고    scopus 로고
    • Finding motifs in the twilight zone
    • Keich, U., Pevzner, P.A.: Finding motifs in the twilight zone. Bioinformatics 18 (2002) 1374-1381
    • (2002) Bioinformatics , vol.18 , pp. 1374-1381
    • Keich, U.1    Pevzner, P.A.2
  • 14
    • 3543073394 scopus 로고    scopus 로고
    • Recognition of multiple patterns in unaligned sets of sequences: Comparison of kernel clustering method with other methods
    • Kel, A., Tikunov, Y., Voss, N., Wingender, E.: Recognition of multiple patterns in unaligned sets of sequences: comparison of kernel clustering method with other methods. Bioinformatics 20 (2004) 1512-1516
    • (2004) Bioinformatics , vol.20 , pp. 1512-1516
    • Kel, A.1    Tikunov, Y.2    Voss, N.3    Wingender, E.4
  • 15
  • 16
    • 27544437350 scopus 로고    scopus 로고
    • Finding exact optimal motifs in matrix representation by partitioning
    • Leung, H.C., Chin, F.Y.: Finding exact optimal motifs in matrix representation by partitioning. Bioinformatics 21 (2005) SII86-92
    • (2005) Bioinformatics , vol.21
    • Leung, H.C.1    Chin, F.Y.2
  • 17
    • 0035228215 scopus 로고    scopus 로고
    • Liu, X., Brutlag, D.L., Liu, J.S.: BioProspector: discovering conserved DNA motifs in upstream regulatory regions of co-expressed genes. Pac. Sym. Biocomp. (PSB'2001) 127-138
    • Liu, X., Brutlag, D.L., Liu, J.S.: BioProspector: discovering conserved DNA motifs in upstream regulatory regions of co-expressed genes. Pac. Sym. Biocomp. (PSB'2001) 127-138
  • 18
    • 0033677426 scopus 로고    scopus 로고
    • Algorithms for extracting structured motifs using a suffix tree with an application to promoter and regulatory site consensus identification
    • Marsan, L., Sagot, M.-F.: Algorithms for extracting structured motifs using a suffix tree with an application to promoter and regulatory site consensus identification. J. Comp. Biol. 7 (2000) 345-362
    • (2000) J. Comp. Biol , vol.7 , pp. 345-362
    • Marsan, L.1    Sagot, M.-F.2
  • 19
    • 0035224579 scopus 로고    scopus 로고
    • An algorithm for finding signals of unknown length in DNA sequences
    • Pavesi, G., Mauri, G., Pesole, G.: An algorithm for finding signals of unknown length in DNA sequences. Bioinformatics 17 (2001) S207-214
    • (2001) Bioinformatics , vol.17
    • Pavesi, G.1    Mauri, G.2    Pesole, G.3
  • 20
    • 0026729501 scopus 로고
    • WORDUP: An efficient algorithm for discovering statistically significant patterns in DNA sequences
    • Pesole, G., Prunella, N., Liuni, S., Attimonelli, M., Saccone, C.: WORDUP: an efficient algorithm for discovering statistically significant patterns in DNA sequences. Nucleic Acids Res. 20 (1992) 2871-2875
    • (1992) Nucleic Acids Res , vol.20 , pp. 2871-2875
    • Pesole, G.1    Prunella, N.2    Liuni, S.3    Attimonelli, M.4    Saccone, C.5
  • 22
    • 2342476143 scopus 로고    scopus 로고
    • Finding subtle motifs by branching from sample strings
    • Price, A., Ramabhadran, S., Pevzner, P.A.: Finding subtle motifs by branching from sample strings. Bioinformatics 19 (2003) SII149-155
    • (2003) Bioinformatics , vol.19
    • Price, A.1    Ramabhadran, S.2    Pevzner, P.A.3
  • 23
    • 0020055592 scopus 로고
    • Improvements to a program for DNA analysis: A procedure to find homologies among many sequences
    • Queen, C., Wegman, M.N., Korn, L. J.: Improvements to a program for DNA analysis: a procedure to find homologies among many sequences. Nucleic Acids Res. 10 (1982) 449-456
    • (1982) Nucleic Acids Res , vol.10 , pp. 449-456
    • Queen, C.1    Wegman, M.N.2    Korn, L.J.3
  • 24
    • 0031684427 scopus 로고    scopus 로고
    • Combinatorial pattern discovery in biological sequences: The TEIRESIAS algorithm
    • Rigoutsos, I., Floratos, A.: Combinatorial pattern discovery in biological sequences: the TEIRESIAS algorithm. Bioinformatics 14 (1998) 55-67
    • (1998) Bioinformatics , vol.14 , pp. 55-67
    • Rigoutsos, I.1    Floratos, A.2
  • 26
    • 0024385974 scopus 로고
    • Methods for discovering novel motifs in nucleic acid sequences
    • Staden, R.: Methods for discovering novel motifs in nucleic acid sequences. Comp. Appl. Biosci. 5 (1989) 293-298
    • (1989) Comp. Appl. Biosci , vol.5 , pp. 293-298
    • Staden, R.1
  • 27
    • 0000133199 scopus 로고
    • Identifying protein-binding sites from unaligned DNA fragments
    • Stormo, G.D., Hartzell, G.W.: Identifying protein-binding sites from unaligned DNA fragments. Proc. Natl. Acad. Sci. USA 86 (1989) 1183-1187
    • (1989) Proc. Natl. Acad. Sci. USA , vol.86 , pp. 1183-1187
    • Stormo, G.D.1    Hartzell, G.W.2
  • 29
    • 0036137323 scopus 로고    scopus 로고
    • A higher-order background model improves the detection of promoter regulatory elements by Gibbs sampling
    • Thijs, G., Lescot, M., Marchai, K., Rombauts, S., De Moor, B., Rouzé, P., Moreau, Y.: A higher-order background model improves the detection of promoter regulatory elements by Gibbs sampling. Bioinformatics 17 (2001) 1113-1122
    • (2001) Bioinformatics , vol.17 , pp. 1113-1122
    • Thijs, G.1    Lescot, M.2    Marchai, K.3    Rombauts, S.4    De Moor, B.5    Rouzé, P.6    Moreau, Y.7
  • 30
    • 0033289316 scopus 로고    scopus 로고
    • An exact method for finding short motifs in sequences, with application to the ribosome binding site problem
    • Tompa, M.: An exact method for finding short motifs in sequences, with application to the ribosome binding site problem. Proc. 7th Int. Conf. Intelligent Systems Mol. Biol. (ISMB'1999) 262-271
    • Proc. 7th Int. Conf. Intelligent Systems Mol. Biol. (ISMB'1999) , pp. 262-271
    • Tompa, M.1
  • 32
    • 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., 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
  • 33
    • 0034656326 scopus 로고    scopus 로고
    • Discovering regulatory elements in noncoding sequences by analysis of spaced dyads
    • van Helden, J., Rios, A.F., Collado-Vides, J.: Discovering regulatory elements in noncoding sequences by analysis of spaced dyads. Nucleic Acids Res. 28 (2000) 1808-1818
    • (2000) Nucleic Acids Res , vol.28 , pp. 1808-1818
    • van Helden, J.1    Rios, A.F.2    Collado-Vides, J.3
  • 34
    • 0021665479 scopus 로고
    • Pattern recognition in several sequences: Consensus and alignment
    • Waterman, M.S., Arratia, R., Galas, D.J.: Pattern recognition in several sequences: consensus and alignment. Bull. Math. Biol. 46 (1984) 515-527
    • (1984) Bull. Math. Biol , vol.46 , pp. 515-527
    • Waterman, M.S.1    Arratia, R.2    Galas, D.J.3
  • 35
    • 0029867505 scopus 로고    scopus 로고
    • Identification of functional elements in unaligned nucleic acid sequences by a novel tuple search algorithm
    • Wolfertstetter, F., Freeh, K., Herrmann, G., Werner, T.: Identification of functional elements in unaligned nucleic acid sequences by a novel tuple search algorithm. Comp. Appl. Biosci. 12 (1996) 71-80
    • (1996) Comp. Appl. Biosci , vol.12 , pp. 71-80
    • Wolfertstetter, F.1    Freeh, K.2    Herrmann, G.3    Werner, T.4
  • 36
    • 0033655171 scopus 로고    scopus 로고
    • Workman, C.T., Stormo, G.D.: ANN-Spec: a method for discovering transcription factor binding sites with improved specificity. Pac. Sym. Biocomp. (PSB'2000) 467-478
    • Workman, C.T., Stormo, G.D.: ANN-Spec: a method for discovering transcription factor binding sites with improved specificity. Pac. Sym. Biocomp. (PSB'2000) 467-478
  • 37
    • 2342445980 scopus 로고    scopus 로고
    • Modeling within-motif dependence for transcription factor binding site predictions
    • Zhou, Q., Liu, J.S.: Modeling within-motif dependence for transcription factor binding site predictions. Bioinformatics 20 (2004) 909-916
    • (2004) Bioinformatics , vol.20 , pp. 909-916
    • Zhou, Q.1    Liu, J.S.2


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