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Volumn 10, Issue , 2009, Pages 323-

A stochastic context free grammar based framework for analysis of protein sequences

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACIDS; BINDING SITES; BIOINFORMATICS; FORMAL LANGUAGES; GENETIC ALGORITHMS; LEARNING SYSTEMS; MOLECULAR BIOLOGY; PATTERN RECOGNITION; PROTEINS; STOCHASTIC SYSTEMS;

EID: 70449635228     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-10-323     Document Type: Article
Times cited : (30)

References (64)
  • 1
    • 0004449398 scopus 로고
    • Three models for the description of language
    • Chomsky N. Three models for the description of language. IRE Trans. on Information Theory IT 1956, 2(3):113-124.
    • (1956) IRE Trans. on Information Theory IT , vol.2 , Issue.3 , pp. 113-124
    • Chomsky, N.1
  • 2
    • 0021760864 scopus 로고
    • Genome structure described by formal languages
    • 10.1093/nar/12.5.2561, 318685, 6200832
    • Brendel V, Busse HG. Genome structure described by formal languages. Nucleic Acid Res 1984, 12:2561-2568. 10.1093/nar/12.5.2561, 318685, 6200832.
    • (1984) Nucleic Acid Res , vol.12 , pp. 2561-2568
    • Brendel, V.1    Busse, H.G.2
  • 3
    • 0000827027 scopus 로고
    • On the syntactic structure of protein sequences and the concept of grammar complexity
    • Jimenez-Montao MA. On the syntactic structure of protein sequences and the concept of grammar complexity. Bull Math Biol 1984, 46:641-659.
    • (1984) Bull Math Biol , vol.46 , pp. 641-659
    • Jimenez-Montao, M.A.1
  • 4
    • 0023494703 scopus 로고
    • Formal language theory and DNA: an analysis of the generative capacity of specific recombinant behaviors
    • Head T. Formal language theory and DNA: an analysis of the generative capacity of specific recombinant behaviors. Bull Math Biol 1987, 49:737-750.
    • (1987) Bull Math Biol , vol.49 , pp. 737-750
    • Head, T.1
  • 5
    • 0037079055 scopus 로고    scopus 로고
    • The language of genes
    • 10.1038/nature01255, 12432405
    • Searls DB. The language of genes. Nature 2002, 420:211-217. 10.1038/nature01255, 12432405.
    • (2002) Nature , vol.420 , pp. 211-217
    • Searls, D.B.1
  • 8
    • 70449647347 scopus 로고    scopus 로고
    • Zastosowanie wnioskowania gramatycznego w analizie biologicznych sekwencji danych
    • Wroclaw University of Technology
    • Maczka J. Zastosowanie wnioskowania gramatycznego w analizie biologicznych sekwencji danych. MSc thesis 2004, Wroclaw University of Technology.
    • (2004) MSc thesis
    • Maczka, J.1
  • 11
    • 70449661158 scopus 로고
    • Building a Knowledge-Base for Protein Function Prediction using Multistrategy Learning
    • Universal Academy Press, Tokyo, Hagiya M, Suyama A, Takagi T, Nakai K, Miyano S, Yokomori T
    • Ishikawa T, Mitaku S, Terano T, Hirokawa T, Suwa M, Ching SB. Building a Knowledge-Base for Protein Function Prediction using Multistrategy Learning. Proceedings of Genome Informatics Workshop: 1995 1995, Universal Academy Press, Tokyo, Hagiya M, Suyama A, Takagi T, Nakai K, Miyano S, Yokomori T.
    • (1995) Proceedings of Genome Informatics Workshop: 1995
    • Ishikawa, T.1    Mitaku, S.2    Terano, T.3    Hirokawa, T.4    Suwa, M.5    Ching, S.B.6
  • 13
  • 15
    • 0028181441 scopus 로고
    • Hidden Markov models in computational biology: Applications to protein modeling
    • 10.1006/jmbi.1994.1104, 8107089
    • Krogh A, Brown M, Mian IS, Sjolander K, Haussler D. Hidden Markov models in computational biology: Applications to protein modeling. J Mol Biol 1994, 235:1501-1531. 10.1006/jmbi.1994.1104, 8107089.
    • (1994) J Mol Biol , vol.235 , pp. 1501-1531
    • Krogh, A.1    Brown, M.2    Mian, I.S.3    Sjolander, K.4    Haussler, D.5
  • 17
    • 33745210056 scopus 로고    scopus 로고
    • Inductive and Statistical Learning of Formal Grammars
    • Research talk at Université catholique de Louvain, Louvain-La-Neuve
    • Dupont PR. Inductive and Statistical Learning of Formal Grammars. 2002, Research talk at Université catholique de Louvain, Louvain-La-Neuve.
    • (2002)
    • Dupont, P.R.1
  • 19
    • 0001926477 scopus 로고
    • The Computational Linguistics of Biological Sequences
    • AAAI Press, Menlo Park, CA, Hunter L
    • Searls DB. The Computational Linguistics of Biological Sequences. Artificial Intelligence and Molecular Biology 1993, 2:47-120. AAAI Press, Menlo Park, CA, Hunter L.
    • (1993) Artificial Intelligence and Molecular Biology , vol.2 , pp. 47-120
    • Searls, D.B.1
  • 20
    • 0003857782 scopus 로고    scopus 로고
    • HMMER User's Guide: Biological sequence analysis using profile hidden Markov models
    • Washington University School of Medicine, Howard Hughes Medical Institute and Dept. of Genetics
    • Eddy S. HMMER User's Guide: Biological sequence analysis using profile hidden Markov models. 2003, Washington University School of Medicine, Howard Hughes Medical Institute and Dept. of Genetics.
    • (2003)
    • Eddy, S.1
  • 21
    • 70449664469 scopus 로고
    • An Algorithm for Estimating the Parameters of Unrestricted Hidden Stochastic Context-Free Grammars
    • Association for Computational Linguistics, Morristown, NJ
    • Kupiec J. An Algorithm for Estimating the Parameters of Unrestricted Hidden Stochastic Context-Free Grammars. Proceedings of the 14th conference on Computational linguistics 1992, 1:387-393. Association for Computational Linguistics, Morristown, NJ.
    • (1992) Proceedings of the 14th conference on Computational linguistics , vol.1 , pp. 387-393
    • Kupiec, J.1
  • 25
    • 42549148061 scopus 로고    scopus 로고
    • RNACompress: Grammar-based compression and informational complexity measurement of RNA secondary structure
    • Liu Q, Yang Y, Chen C, Bu J, Zhang Y, Ye X. RNACompress: Grammar-based compression and informational complexity measurement of RNA secondary structure. BMC Bioinformatics 2008, 9(176).
    • (2008) BMC Bioinformatics , vol.9 , Issue.176
    • Liu, Q.1    Yang, Y.2    Chen, C.3    Bu, J.4    Zhang, Y.5    Ye, X.6
  • 26
    • 49949150022 scopus 로고
    • Language identification in the limit
    • Gold EM. Language identification in the limit. Information and Control 1967, 10(5):447-474.
    • (1967) Information and Control , vol.10 , Issue.5 , pp. 447-474
    • Gold, E.M.1
  • 27
    • 0026839284 scopus 로고
    • Efficient learning of context-free grammars from positive structural examples
    • Sakakibara Y. Efficient learning of context-free grammars from positive structural examples. Inform Comput 1992, 97:23-60.
    • (1992) Inform Comput , vol.97 , pp. 23-60
    • Sakakibara, Y.1
  • 31
    • 0000353178 scopus 로고
    • A maximization technique occurring in the statistical analysis of probabilistic functions of Markov chains
    • Baum LE, Petrie T, Soules G, Weiss N. A maximization technique occurring in the statistical analysis of probabilistic functions of Markov chains. Ann Math Statist 1970, 41(1):164-171.
    • (1970) Ann Math Statist , vol.41 , Issue.1 , pp. 164-171
    • Baum, L.E.1    Petrie, T.2    Soules, G.3    Weiss, N.4
  • 32
    • 0015600423 scopus 로고
    • The Viterbi algorithm
    • Forney GD. The Viterbi algorithm. Proceedings of the IEEE 1973, 61(3):268-278.
    • (1973) Proceedings of the IEEE , vol.61 , Issue.3 , pp. 268-278
    • Forney, G.D.1
  • 36
    • 0031269127 scopus 로고    scopus 로고
    • Predicting Protein Secondary Structure Using Stochastic Tree Grammars
    • Abe N, Mamitsuka H. Predicting Protein Secondary Structure Using Stochastic Tree Grammars. Machine Learning 1997, 29(2-3):275-301.
    • (1997) Machine Learning , vol.29 , Issue.2-3 , pp. 275-301
    • Abe, N.1    Mamitsuka, H.2
  • 37
    • 0032796501 scopus 로고    scopus 로고
    • RNA secondary structure prediction using stochastic context-free grammars and evolutionary history
    • 10.1093/bioinformatics/15.6.446, 10383470
    • Knudsen B, Hein J. RNA secondary structure prediction using stochastic context-free grammars and evolutionary history. Bioinformatics 1999, 15(6):446-454. 10.1093/bioinformatics/15.6.446, 10383470.
    • (1999) Bioinformatics , vol.15 , Issue.6 , pp. 446-454
    • Knudsen, B.1    Hein, J.2
  • 38
    • 11244339717 scopus 로고    scopus 로고
    • Learning Context-Free Grammars using an Evolutionary Approach
    • University of Maribor and the University of Alabama at Birmingham
    • Mernik M, Crepinsek M, Gerlic G, Zumer V, Viljem Z, Bryant BR, Sprague A. Learning Context-Free Grammars using an Evolutionary Approach. Technical report 2003, University of Maribor and the University of Alabama at Birmingham.
    • (2003) Technical report
    • Mernik, M.1    Crepinsek, M.2    Gerlic, G.3    Zumer, V.4    Viljem, Z.5    Bryant, B.R.6    Sprague, A.7
  • 39
    • 19944376889 scopus 로고    scopus 로고
    • Learning context-free grammars using tabular representations
    • Sakakibara Y. Learning context-free grammars using tabular representations. Pattern Recognition 2005, 38:1372-1383.
    • (2005) Pattern Recognition , vol.38 , pp. 1372-1383
    • Sakakibara, Y.1
  • 40
    • 19844378930 scopus 로고    scopus 로고
    • Evolutionary induction of stochastic context free grammars
    • Keller B, Lutz R. Evolutionary induction of stochastic context free grammars. Pattern Recognition 2005, 38:1393-1406.
    • (2005) Pattern Recognition , vol.38 , pp. 1393-1406
    • Keller, B.1    Lutz, R.2
  • 41
    • 70449688689 scopus 로고    scopus 로고
    • Rozpoznawanie wzorców proteinowych z zastosowaniem metod maszynowego uczenia
    • Wroclaw University of Technology
    • Dyrka W. Rozpoznawanie wzorców proteinowych z zastosowaniem metod maszynowego uczenia. MSc thesis 2005, Wroclaw University of Technology.
    • (2005) MSc thesis
    • Dyrka, W.1
  • 42
    • 70449647346 scopus 로고    scopus 로고
    • Zastosowanie ewolucyjnie modyfikowanych Maszyn Turinga w rozpoznawaniu biosekwencji
    • Wroclaw University of Technology
    • Wadowski D. Zastosowanie ewolucyjnie modyfikowanych Maszyn Turinga w rozpoznawaniu biosekwencji. MSc thesis 2004, Wroclaw University of Technology.
    • (2004) MSc thesis
    • Wadowski, D.1
  • 43
    • 0024046665 scopus 로고    scopus 로고
    • Cluster analysis of amino acid indices for prediction of protein structure and function
    • Nakai K, Kidera A, Kanehisa M. Cluster analysis of amino acid indices for prediction of protein structure and function. Protein Eng 1998, 2:93-100.
    • (1998) Protein Eng , vol.2 , pp. 93-100
    • Nakai, K.1    Kidera, A.2    Kanehisa, M.3
  • 44
    • 0029922443 scopus 로고    scopus 로고
    • Analysis of amino acid indices and mutation matrices for sequence comparison and structure prediction of proteins
    • 10.1093/protein/9.1.27, 9053899
    • Tomii K, Kanehisa M. Analysis of amino acid indices and mutation matrices for sequence comparison and structure prediction of proteins. Protein Eng 1996, 9:27-36. 10.1093/protein/9.1.27, 9053899.
    • (1996) Protein Eng , vol.9 , pp. 27-36
    • Tomii, K.1    Kanehisa, M.2
  • 45
    • 0032892577 scopus 로고    scopus 로고
    • AAindex: amino acid index database
    • 10.1093/nar/27.1.368, 148186, 9847231
    • Kawashima S, Ogata H, Kanehisa M. AAindex: amino acid index database. Nucleic Acids Res 1999, 27:368-369. 10.1093/nar/27.1.368, 148186, 9847231.
    • (1999) Nucleic Acids Res , vol.27 , pp. 368-369
    • Kawashima, S.1    Ogata, H.2    Kanehisa, M.3
  • 46
    • 0019065166 scopus 로고
    • Local hydrophobicity stabilizes secondary structures in proteins
    • 10.1002/bip.1980.360190906, 7426680
    • Kanehisa MI, Tsong TY. Local hydrophobicity stabilizes secondary structures in proteins. Biopolymers 1980, 19:1617-1628. 10.1002/bip.1980.360190906, 7426680.
    • (1980) Biopolymers , vol.19 , pp. 1617-1628
    • Kanehisa, M.I.1    Tsong, T.Y.2
  • 47
    • 0017105767 scopus 로고
    • Conformational properties of amino acid residues in globular proteins
    • 10.1016/S0022-2836(76)80008-3, 1003471
    • Robson B, Suzuki E. Conformational properties of amino acid residues in globular proteins. J Mol Biol 1976, 107:327-356. 10.1016/S0022-2836(76)80008-3, 1003471.
    • (1976) J Mol Biol , vol.107 , pp. 327-356
    • Robson, B.1    Suzuki, E.2
  • 50
    • 0023718983 scopus 로고
    • Secondary structure prediction: combination of three different methods
    • 10.1093/protein/2.3.185, 3237683
    • Biou V, Gibrat JF, Levin JM, Robson B, Garnier J. Secondary structure prediction: combination of three different methods. Protein Eng 1988, 2:185-191. 10.1093/protein/2.3.185, 3237683.
    • (1988) Protein Eng , vol.2 , pp. 185-191
    • Biou, V.1    Gibrat, J.F.2    Levin, J.M.3    Robson, B.4    Garnier, J.5
  • 51
    • 0021772378 scopus 로고
    • Prediction of protein function from sequence properties: Discriminant analysis of a data base
    • Klein P, Kanehisa M, DeLisi C. Prediction of protein function from sequence properties: Discriminant analysis of a data base. Biochim Biophys Acta 1984, 787:221-226.
    • (1984) Biochim Biophys Acta , vol.787 , pp. 221-226
    • Klein, P.1    Kanehisa, M.2    DeLisi, C.3
  • 54
    • 70449664470 scopus 로고    scopus 로고
    • GAlib library documentation (version 2.4.4)
    • Massachusetts Institute of Technology
    • Wall M. GAlib library documentation (version 2.4.4). 1999, Massachusetts Institute of Technology.
    • (1999)
    • Wall, M.1
  • 55
    • 70449694628 scopus 로고    scopus 로고
    • Probabilistic Context-Free Grammar for pattern detection in protein sequences
    • Kingston University, London
    • Dyrka W. Probabilistic Context-Free Grammar for pattern detection in protein sequences. MSc thesis 2007, Kingston University, London.
    • (2007) MSc thesis
    • Dyrka, W.1
  • 57
    • 33846041078 scopus 로고    scopus 로고
    • Universal Protein Resource (UniProt)
    • 10.1093/nar/gkl929, 1669721, 17142230
    • UniProt Consortium Universal Protein Resource (UniProt). Nucleic Acid Res 2007, 35:D193-D197. 10.1093/nar/gkl929, 1669721, 17142230.
    • (2007) Nucleic Acid Res , vol.35
  • 59
    • 0028922586 scopus 로고
    • LIGPLOT: A program to generate schematic diagrams of protein-ligand interactions
    • 10.1093/protein/8.2.127, 7630882
    • Wallace AC, Laskowski RA, Thornton JM. LIGPLOT: A program to generate schematic diagrams of protein-ligand interactions. Protein Eng 1995, 8:127-134. 10.1093/protein/8.2.127, 7630882.
    • (1995) Protein Eng , vol.8 , pp. 127-134
    • Wallace, A.C.1    Laskowski, R.A.2    Thornton, J.M.3
  • 60
    • 0005654493 scopus 로고
    • On the inverse relationship of Recall and Precision
    • Cleverdon CW. On the inverse relationship of Recall and Precision. Journal of Documentation 1972, 28:195-201.
    • (1972) Journal of Documentation , vol.28 , pp. 195-201
    • Cleverdon, C.W.1
  • 62
    • 0030721639 scopus 로고    scopus 로고
    • Structural alignment of the (+)-trans-anti-benzo[a]pyrene-dG adduct positioned opposite dC at a DNA template primer junction
    • 10.1021/bi970069s, 9374853
    • Feng B, Gorin AA, Hingerty BE, Geacintov NE, Broyde S, Patel DJ. Structural alignment of the (+)-trans-anti-benzo[a]pyrene-dG adduct positioned opposite dC at a DNA template primer junction. Biochemistry 1997, 36:13769-13779. 10.1021/bi970069s, 9374853.
    • (1997) Biochemistry , vol.36 , pp. 13769-13779
    • Feng, B.1    Gorin, A.A.2    Hingerty, B.E.3    Geacintov, N.E.4    Broyde, S.5    Patel, D.J.6
  • 64
    • 0018110116 scopus 로고
    • Prediction of the secondary structure of proteins from their amino acid sequence
    • Chou PY, Fasman GD. Prediction of the secondary structure of proteins from their amino acid sequence. J Adv Enzymol 1978, 47:45-148.
    • (1978) J Adv Enzymol , vol.47 , pp. 45-148
    • Chou, P.Y.1    Fasman, G.D.2


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