메뉴 건너뛰기




Volumn 19, Issue SUPPL. 2, 2003, Pages

HMM sampling and applications to gene finding and alternative splicing

Author keywords

Conserved alternative splicing; Hidden Markov model; Sampling; Suboptimal parses

Indexed keywords

ALGORITHM; ALTERNATIVE RNA SPLICING; CODON; CONFERENCE PAPER; DNA SEQUENCE; EXON; GENE STRUCTURE; HUMAN; MATHEMATICAL ANALYSIS; NONHUMAN; PRIORITY JOURNAL; PROBABILITY; SEQUENCE ALIGNMENT;

EID: 2942610553     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/btg1057     Document Type: Conference Paper
Times cited : (57)

References (34)
  • 1
    • 0037350957 scopus 로고    scopus 로고
    • SLAM - Cross-species genefinding and alignment wihth a generalized pair hidden Markov model
    • Alexandersson, M., Cawley, S. and Pachter, L. (2003) SLAM - Cross-species genefinding and alignment wihth a generalized pair hidden Markov model. Genome Res., 13, 496-502.
    • (2003) Genome Res. , vol.13 , pp. 496-502
    • Alexandersson, M.1    Cawley, S.2    Pachter, L.3
  • 2
    • 0000386998 scopus 로고
    • On Kth best policies
    • Bellman, R. and Kalaba, R. (1960) On Kth best policies. J. SIAM, 8(4), 582-588.
    • (1960) J. SIAM , vol.8 , Issue.4 , pp. 582-588
    • Bellman, R.1    Kalaba, R.2
  • 3
    • 0001019232 scopus 로고
    • Computing the N best loopless paths in a network
    • Clarke, S., Krikorian, A. and Rausen, J. (1963) Computing the N best loopless paths in a network. J. SIAM., 11(4), 1096-1102.
    • (1963) J. SIAM , vol.11 , Issue.4 , pp. 1096-1102
    • Clarke, S.1    Krikorian, A.2    Rausen, J.3
  • 5
    • 0029174347 scopus 로고
    • Multiple alignment using hidden Markov models
    • Eddy, S. R. (1995) Multiple alignment using hidden Markov models. In ISMB-95. 3, pp. 114-120.
    • (1995) ISMB-95 , vol.3 , pp. 114-120
    • Eddy, S.R.1
  • 6
    • 0015585263 scopus 로고
    • Calculating the Kth shortest paths
    • Fox, B. (1973) Calculating the Kth shortest paths. Can. J. Oper. Res. Inf. Process., 11, 66-70.
    • (1973) Can. J. Oper. Res. Inf. Process. , vol.11 , pp. 66-70
    • Fox, B.1
  • 8
    • 0016518550 scopus 로고
    • A linear space algorithm for computing maximal common subsequences
    • Hirschberg, D. S. (1975) A linear space algorithm for computing maximal common subsequences. Commun. ACM, 18(6), 341-343.
    • (1975) Commun. ACM , vol.18 , Issue.6 , pp. 341-343
    • Hirschberg, D.S.1
  • 9
    • 0001681038 scopus 로고
    • A method for the solution of the Nth best path problem
    • Hoffman, W. and Pavley, R. (1959) A method for the solution of the Nth best path problem. J. ACM, 6, 506-514.
    • (1959) J. ACM , vol.6 , pp. 506-514
    • Hoffman, W.1    Pavley, R.2
  • 11
    • 0035036534 scopus 로고    scopus 로고
    • Gene structure prediction and alternative splicing analysis using genomically aligned ESTs
    • Kan, Z., Rouchka, E.C., Gis, W.R. and States, D.J. (2001) Gene structure prediction and alternative splicing analysis using genomically aligned ESTs. Genome Res., 11, 889-900.
    • (2001) Genome Res. , vol.11 , pp. 889-900
    • Kan, Z.1    Rouchka, E.C.2    Gis, W.R.3    States, D.J.4
  • 12
    • 0000685484 scopus 로고
    • A Procedure for computing the K-best solutions to discrete optimization problems and its appplications to the shortest paths problem
    • Lawler, E. L. (1972) A Procedure for computing the K-best solutions to discrete optimization problems and its appplications to the shortest paths problem. Manage. Sci., 18, 401-405.
    • (1972) Manage. Sci. , vol.18 , pp. 401-405
    • Lawler, E.L.1
  • 13
    • 0036337915 scopus 로고    scopus 로고
    • A genomic view of alternative splicing
    • Modrek, B. and Lee, C. (2002) A genomic view of alternative splicing. Nat. Genet, 30, 13-19.
    • (2002) Nat. Genet , vol.30 , pp. 13-19
    • Modrek, B.1    Lee, C.2
  • 15
    • 0028679401 scopus 로고
    • On near-optimal alignments of biological sequences
    • Naor, D. and Brutlag, D.L. (1994) On near-optimal alignments of biological sequences. J. Comput. Biol., 1(4), 349-366.
    • (1994) J. Comput. Biol. , vol.1 , Issue.4 , pp. 349-366
    • Naor, D.1    Brutlag, D.L.2
  • 16
    • 0014757386 scopus 로고
    • A general method applicable to the search for similarities in the amino acid sequence of two proteins
    • Needleman, S.B. and Wunsch, C.D. (1970) A general method applicable to the search for similarities in the amino acid sequence of two proteins. J. Mol. Biol., 48, 443-453.
    • (1970) J. Mol. Biol. , vol.48 , pp. 443-453
    • Needleman, S.B.1    Wunsch, C.D.2
  • 17
    • 0142104045 scopus 로고    scopus 로고
    • Analysis of the mouse transcriptome based on functional annotation of 60770 full-length cDNAs
    • Okazaki, Y. et al. (2002) Analysis of the mouse transcriptome based on functional annotation of 60770 full-length cDNAs. Nature, 420, 563-573.
    • (2002) Nature , vol.420 , pp. 563-573
    • Okazaki, Y.1
  • 19
    • 0022726286 scopus 로고
    • Implementation of algorithms for K shortest loopless paths
    • Perko, A. (1986) Implementation of algorithms for K shortest loopless paths. Networks, 16, 149-160.
    • (1986) Networks , vol.16 , pp. 149-160
    • Perko, A.1
  • 20
    • 0004524167 scopus 로고
    • The kth best route through a network
    • Pollack, M. (1961) The kth best route through a network. Oper. Res., 9(4), 578-580.
    • (1961) Oper. Res. , vol.9 , Issue.4 , pp. 578-580
    • Pollack, M.1
  • 21
    • 0034022596 scopus 로고    scopus 로고
    • Genie-gene finding in Drosophila melanogaster
    • Reese, M.G., Kulp, D., Tammana, H. and Haussler, D. (2000) Genie-gene finding in Drosophila melanogaster. Genome Res., 10(4), 529-538.
    • (2000) Genome Res. , vol.10 , Issue.4 , pp. 529-538
    • Reese, M.G.1    Kulp, D.2    Tammana, H.3    Haussler, D.4
  • 22
    • 0025913421 scopus 로고
    • A simple method to generate non-trivial alternate alignments of protein sequences
    • Saqi, M.A.S. and Sternberg, M. (1991) A simple method to generate non-trivial alternate alignments of protein sequences. J. Mol. Biol., 219, 727-732.
    • (1991) J. Mol. Biol. , vol.219 , pp. 727-732
    • Saqi, M.A.S.1    Sternberg, M.2
  • 23
    • 0026632962 scopus 로고
    • Towards an automatic method of predicting protein structure by homology: An evaluation of suboptimal sequence alignments
    • Saqi, M.A.S., Bates, P. and Sternberg, M.J.E. (1992) Towards an automatic method of predicting protein structure by homology: an evaluation of suboptimal sequence alignments. Protein Eng., 5(4), 305-311.
    • (1992) Protein Eng. , vol.5 , Issue.4 , pp. 305-311
    • Saqi, M.A.S.1    Bates, P.2    Sternberg, M.J.E.3
  • 24
    • 0018518940 scopus 로고
    • On algorithms for finding the K shortest paths in a network
    • Shier, D.R. (1979) On algorithms for finding the K shortest paths in a network. Networks, 9, 195-214.
    • (1979) Networks , vol.9 , pp. 195-214
    • Shier, D.R.1
  • 25
    • 0029196976 scopus 로고
    • Recursive dynamic programming for adaptive sequence and structure alignment
    • Thiele, R., Zimmer, R. and Lengauer, T. (1995) Recursive dynamic programming for adaptive sequence and structure alignment. In ISMB-95. 3, pp. 384-392.
    • (1995) ISMB-95 , vol.3 , pp. 384-392
    • Thiele, R.1    Zimmer, R.2    Lengauer, T.3
  • 26
    • 0025372332 scopus 로고
    • Determination of reliable regions in protein sequence alignments
    • Vingron, M. and Argos, P. (1990) Determination of reliable regions in protein sequence alignments. Protein Eng., 3, 565-569.
    • (1990) Protein Eng. , vol.3 , pp. 565-569
    • Vingron, M.1    Argos, P.2
  • 27
    • 0013549381 scopus 로고
    • Sequence alignments in the neighborhood of the optimum with general application to dynamic programming
    • Waterman, M.S. (1983) Sequence alignments in the neighborhood of the optimum with general application to dynamic programming. Proc. Natl Acad. Sci. USA, 80, 3123-3124.
    • (1983) Proc. Natl. Acad. Sci. USA , vol.80 , pp. 3123-3124
    • Waterman, M.S.1
  • 28
    • 0023661088 scopus 로고
    • A new algorithm for best subsequence alignments with application to tRNA-rRNA comparisons
    • Waterman, M.S. and Eggert, M. (1987) A new algorithm for best subsequence alignments with application to tRNA-rRNA comparisons. J. Mol. Biol., 197, 723-728.
    • (1987) J. Mol. Biol. , vol.197 , pp. 723-728
    • Waterman, M.S.1    Eggert, M.2
  • 29
    • 0022380106 scopus 로고
    • A dynamic programming algorithm to find all solutions in a neighborhood of the optimum
    • Waterman, M.S. and Byers, T.H. (1985) A dynamic programming algorithm to find all solutions in a neighborhood of the optimum. Math. Biosci., 77, 179-188.
    • (1985) Math. Biosci. , vol.77 , pp. 179-188
    • Waterman, M.S.1    Byers, T.H.2
  • 31
    • 0028464982 scopus 로고
    • Parametric and ensemble sequence alignment algorithms
    • Waterman, M.S. (1994) Parametric and ensemble sequence alignment algorithms. Bull. Math. Biol., 56(4), 743-767.
    • (1994) Bull. Math. Biol. , vol.56 , Issue.4 , pp. 743-767
    • Waterman, M.S.1
  • 32
    • 1542563409 scopus 로고    scopus 로고
    • Initial sequencing and comparative analysis of the mouse genome
    • Waterston, R.H. et al. (2002) Initial sequencing and comparative analysis of the mouse genome. Nature, 420, 520-562.
    • (2002) Nature , vol.420 , pp. 520-562
    • Waterston, R.H.1
  • 33
    • 0031874740 scopus 로고    scopus 로고
    • Bayesian adaptive sequence alignment algorithms
    • Zhu, J., Liu, J.S. and Lawrence, C.E. (1998) Bayesian adaptive sequence alignment algorithms. Bioinformatics, 14, 25-39.
    • (1998) Bioinformatics , vol.14 , pp. 25-39
    • Zhu, J.1    Liu, J.S.2    Lawrence, C.E.3
  • 34
    • 0025800635 scopus 로고
    • Suboptimal sequence alignment in molecular biology: Alignment with error analysis
    • Zuker, M. (1991) Suboptimal sequence alignment in molecular biology: alignment with error analysis. J. Mol. Biol., 221, 403-420.
    • (1991) J. Mol. Biol. , vol.221 , pp. 403-420
    • Zuker, M.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.