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Volumn 3909 LNBI, Issue , 2006, Pages 160-174

CONTRAlign: Discriminative training for protein sequence alignment

Author keywords

[No Author keywords available]

Indexed keywords

AUTOMATION; BIOCOMMUNICATIONS; INFORMATION THEORY; LEARNING SYSTEMS; MATRIX ALGEBRA; PERSONNEL TRAINING;

EID: 33745783706     PISSN: 03029743     EISSN: 16113349     Source Type: Book Series    
DOI: 10.1007/11732990_15     Document Type: Conference Paper
Times cited : (58)

References (44)
  • 1
    • 0032962457 scopus 로고    scopus 로고
    • Twilight zone of protein sequence alignments
    • Rost, B.: Twilight zone of protein sequence alignments. Protein Eng 12 (1999) 85-94
    • (1999) Protein Eng , vol.12 , pp. 85-94
    • Rost, B.1
  • 2
    • 2942619012 scopus 로고    scopus 로고
    • SDCoffee: Combining protein sequences and structures within multiple sequence alignments
    • O'Sullivan, O., Suhre, K., Abergel, C., Higgins, D.G., Notredame, C.: SDCoffee: combining protein sequences and structures within multiple sequence alignments. J Mol Biol 340 (2004) 385-395
    • (2004) J Mol Biol , vol.340 , pp. 385-395
    • O'Sullivan, O.1    Suhre, K.2    Abergel, C.3    Higgins, D.G.4    Notredame, C.5
  • 3
    • 0035967880 scopus 로고    scopus 로고
    • FUGUE: Sequence-structure homology recognition using environment-specific substitution tables and structure-dependent gap penalties
    • Shi, J., Blundell, T.L., Mizuguchi, K.: FUGUE: sequence-structure homology recognition using environment-specific substitution tables and structure-dependent gap penalties. J Mol Biol 310 (2001) 243-257
    • (2001) J Mol Biol , vol.310 , pp. 243-257
    • Shi, J.1    Blundell, T.L.2    Mizuguchi, K.3
  • 4
    • 0024349252 scopus 로고
    • Protein structure alignment
    • Taylor, W.R., Orengo, C.A.: Protein structure alignment. J Mol Biol 208 (1989) 1-22
    • (1989) J Mol Biol , vol.208 , pp. 1-22
    • Taylor, W.R.1    Orengo, C.A.2
  • 5
    • 12944249776 scopus 로고
    • A discussion of the solution for the best rotation to relate two sets of vectors
    • Kabsch, W.: A discussion of the solution for the best rotation to relate two sets of vectors. Acta Crystallog Sect A 34 (1978) 827-828
    • (1978) Acta Crystallog Sect A , vol.34 , pp. 827-828
    • Kabsch, W.1
  • 8
    • 24644512819 scopus 로고    scopus 로고
    • SPEM: Improving multiple sequence alignment with sequence profiles and predicted secondary structures
    • Zhou, H., Zhou, Y.: SPEM: improving multiple sequence alignment with sequence profiles and predicted secondary structures. Bioinformatics 21 (2005) 3615-3621
    • (2005) Bioinformatics , vol.21 , pp. 3615-3621
    • Zhou, H.1    Zhou, Y.2
  • 9
    • 0033578684 scopus 로고    scopus 로고
    • Protein secondary structure prediction based on position-specific scoring matrices
    • Jones, D.T.: Protein secondary structure prediction based on position-specific scoring matrices. J Mol Biol 292 (1999) 195-202
    • (1999) J Mol Biol , vol.292 , pp. 195-202
    • Jones, D.T.1
  • 10
    • 23144440940 scopus 로고    scopus 로고
    • PRALINE: A multiple alignment toolbox that integrates homology-extended and secondary structure information
    • Web Server issue
    • Simossis, V.A., Heringa, J.: PRALINE: A multiple alignment toolbox that integrates homology-extended and secondary structure information. Nucleic Acids Res 33 (Web Server issue) (2005) W289-W294
    • (2005) Nucleic Acids Res , vol.33
    • Simossis, V.A.1    Heringa, J.2
  • 11
    • 0026458378 scopus 로고
    • Amino acid substitution matrices from protein blocks
    • Henikoff, S., Henikoff, J.G.: Amino acid substitution matrices from protein blocks. Proc Nat Acad Sci USA 89 (1992) 10915-10919
    • (1992) Proc Nat Acad Sci USA , vol.89 , pp. 10915-10919
    • Henikoff, S.1    Henikoff, J.G.2
  • 12
    • 0028047892 scopus 로고
    • Sequence alignment and penalty choice. Review of concepts, case studies and implications
    • Vingron, M., Waterman, M.S.: Sequence alignment and penalty choice. Review of concepts, case studies and implications. J Mol Biol 235 (1994) 1-12
    • (1994) J Mol Biol , vol.235 , pp. 1-12
    • Vingron, M.1    Waterman, M.S.2
  • 13
    • 85164392958 scopus 로고
    • A study of cross-validation and bootstrap for accuracy estimation and model selection
    • Kohavi, R.: A study of cross-validation and bootstrap for accuracy estimation and model selection. In: IJCAI. (1995) 1137-1145
    • (1995) IJCAI , pp. 1137-1145
    • Kohavi, R.1
  • 15
    • 0142192295 scopus 로고    scopus 로고
    • Conditional random fields: Probabilistic models for segmenting and labeling sequence data
    • Lafferty, J., McCallum, A., Pereira, F.: Conditional random fields: probabilistic models for segmenting and labeling sequence data. In: Proc. 18th ICML. (2001) 282-289
    • (2001) Proc. 18th ICML , pp. 282-289
    • Lafferty, J.1    McCallum, A.2    Pereira, F.3
  • 18
    • 0025878149 scopus 로고
    • Amino acid substitution matrices from an information theoretic perspective
    • Altschul, S.F.: Amino acid substitution matrices from an information theoretic perspective. J Mol Biol 219 (1991) 555-565
    • (1991) J Mol Biol , vol.219 , pp. 555-565
    • Altschul, S.F.1
  • 19
    • 0031721576 scopus 로고    scopus 로고
    • Dynamic programming alignment accuracy
    • Holmes, I., Durbin, R.: Dynamic programming alignment accuracy. J Comp Biol 5 (1998) 493-504
    • (1998) J Comp Biol , vol.5 , pp. 493-504
    • Holmes, I.1    Durbin, R.2
  • 20
    • 14644430471 scopus 로고    scopus 로고
    • PROBCONS: Probabilistic consistency-based multiple sequence alignment
    • Do, C.B., Mahabhashyam, M.S., Brudno, M., Batzoglou, S.: PROBCONS: probabilistic consistency-based multiple sequence alignment. Genome Res 15 (2005) 330-340
    • (2005) Genome Res , vol.15 , pp. 330-340
    • Do, C.B.1    Mahabhashyam, M.S.2    Brudno, M.3    Batzoglou, S.4
  • 21
    • 59549087165 scopus 로고    scopus 로고
    • On discriminative vs. generative classifiers: A comparison of logistic regression and naive Bayes
    • Ng, A., Jordan, M.: On discriminative vs. generative classifiers: a comparison of logistic regression and naive Bayes. In: NIPS 14. (2002)
    • (2002) NIPS , vol.14
    • Ng, A.1    Jordan, M.2
  • 22
    • 0033168097 scopus 로고    scopus 로고
    • A comprehensive comparison of multiple sequence alignment programs
    • Thompson, J.D., Plewniak, F., Poch, O.: A comprehensive comparison of multiple sequence alignment programs. Nucleic Acids Res 27 (1999) 2682-2690
    • (1999) Nucleic Acids Res , vol.27 , pp. 2682-2690
    • Thompson, J.D.1    Plewniak, F.2    Poch, O.3
  • 23
    • 3042666256 scopus 로고    scopus 로고
    • MUSCLE: Multiple sequence alignment with high accuracy and high throughput
    • Edgar, R.C.: MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32 (2004) 1792-1797
    • (2004) Nucleic Acids Res , vol.32 , pp. 1792-1797
    • Edgar, R.C.1
  • 24
    • 44849098451 scopus 로고    scopus 로고
    • A conditional random field for discriminatively-trained finite-state string edit distance
    • McCallum, A., Bellare, K., Pereira, F.: A conditional random field for discriminatively-trained finite-state string edit distance. In: Proc. UAI. (2005)
    • (2005) Proc. UAI
    • McCallum, A.1    Bellare, K.2    Pereira, F.3
  • 28
    • 0027968068 scopus 로고
    • CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties, and weight matrix choice
    • Thompson, J.D., Higgins, D.G., Gibson, T.J.: CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties, and weight matrix choice. Nucleic Acids Res 22 (1994) 4673-4680
    • (1994) Nucleic Acids Res , vol.22 , pp. 4673-4680
    • Thompson, J.D.1    Higgins, D.G.2    Gibson, T.J.3
  • 31
    • 0038278386 scopus 로고    scopus 로고
    • Hidden markov models that use predicted local structure for fold recognition: Alphabets of backbone geometry
    • Karchin, R., Cline, M., Mandel-Guttfreund, Y., Karplus, K.: Hidden markov models that use predicted local structure for fold recognition: alphabets of backbone geometry. Proteins: Structure, Function, and Genetics 51 (2003) 504-514
    • (2003) Proteins: Structure, Function, and Genetics , vol.51 , pp. 504-514
    • Karchin, R.1    Cline, M.2    Mandel-Guttfreund, Y.3    Karplus, K.4
  • 32
    • 24644457706 scopus 로고    scopus 로고
    • BAHBASE 3.0: Latest developments of the multiple sequence alignment benchmark
    • Thompson, J.D., Koehl, P., Ripp, R., Poch, O.: BAHBASE 3.0: latest developments of the multiple sequence alignment benchmark. Proteins 61 (2005) 127-136
    • (2005) Proteins , vol.61 , pp. 127-136
    • Thompson, J.D.1    Koehl, P.2    Ripp, R.3    Poch, O.4
  • 33
    • 16344394781 scopus 로고    scopus 로고
    • SABmark-a benchmark for sequence alignment that covers the entire known fold space
    • Walle, I.V., Lasters, I., Wyns, L.: SABmark-a benchmark for sequence alignment that covers the entire known fold space. Bioinformatics 21 (2005) 1267-1268
    • (2005) Bioinformatics , vol.21 , pp. 1267-1268
    • Walle, I.V.1    Lasters, I.2    Wyns, L.3
  • 34
    • 0028961335 scopus 로고
    • SCOP: A structural classification of proteins database for the investigation of sequences and structures
    • Murzin, A.G., Brenner, S.E., T., H., C., C.: SCOP: a structural classification of proteins database for the investigation of sequences and structures. J Mol Biol 247 (1995) 536-540
    • (1995) J Mol Biol , vol.247 , pp. 536-540
    • Murzin, A.G.1    Brenner, S.E.2    H., T.3    C., C.4
  • 35
    • 0037251892 scopus 로고    scopus 로고
    • NCBI Reference Sequence project: Update and current status
    • Pruitt, K.D., Tatusova, T., Maglott, D.R.: NCBI Reference Sequence project: update and current status. Nucleic Acids Res 31 (2003) 34-37
    • (2003) Nucleic Acids Res , vol.31 , pp. 34-37
    • Pruitt, K.D.1    Tatusova, T.2    Maglott, D.R.3
  • 36
    • 0031766401 scopus 로고    scopus 로고
    • HOMSTRAD: A database of protein structure alignments for homologous familes
    • Mizuguchi, K., Deane, C.M., Blundell, T.L., Overington, J.P.: HOMSTRAD: a database of protein structure alignments for homologous familes. Protein Sci 7 (1998) 2469-2471
    • (1998) Protein Sci , vol.7 , pp. 2469-2471
    • Mizuguchi, K.1    Deane, C.M.2    Blundell, T.L.3    Overington, J.P.4
  • 38
    • 0037100671 scopus 로고    scopus 로고
    • MAFFT: A novel method for rapid multiple sequence alignment based on fast fourier transform
    • Katoh, K., Misawa, K., Kuma, K., Miyata, T.: MAFFT: a novel method for rapid multiple sequence alignment based on fast fourier transform. Nucleic Acids Res 30 (2002) 3059-3066
    • (2002) Nucleic Acids Res , vol.30 , pp. 3059-3066
    • Katoh, K.1    Misawa, K.2    Kuma, K.3    Miyata, T.4
  • 39
    • 13744252890 scopus 로고    scopus 로고
    • MAFFT version 5: Improvement in accuracy of multiple sequence alignment
    • Katoh, K., Kuma, K., Toh, H., Miyata, T.: MAFFT version 5: improvement in accuracy of multiple sequence alignment. Nucleic Acids Res 33 (2005) 511-518
    • (2005) Nucleic Acids Res , vol.33 , pp. 511-518
    • Katoh, K.1    Kuma, K.2    Toh, H.3    Miyata, T.4
  • 40
    • 0034623005 scopus 로고    scopus 로고
    • T-Coffee: A novel method for multiple sequence alignments
    • Notredame, C., Higgins, D., Heringa, J.: T-Coffee: a novel method for multiple sequence alignments. J Mol Biol 302 (2000) 205-217
    • (2000) J Mol Biol , vol.302 , pp. 205-217
    • Notredame, C.1    Higgins, D.2    Heringa, J.3
  • 41
    • 0035984476 scopus 로고    scopus 로고
    • Local weighting schemes for protein multiple sequence alignment
    • Heringa, J.: Local weighting schemes for protein multiple sequence alignment. Computers and Chemistry 26 (2002) 459-477
    • (2002) Computers and Chemistry , vol.26 , pp. 459-477
    • Heringa, J.1
  • 42
    • 33745766339 scopus 로고    scopus 로고
    • MUSCLE: Low-complexity multiple sequence alignment with T-Coffee accuracy
    • Edgar, R.C.: MUSCLE: low-complexity multiple sequence alignment with T-Coffee accuracy. In: ISMB/ECCB. (2004)
    • (2004) ISMB/ECCB
    • Edgar, R.C.1
  • 43
    • 1242320272 scopus 로고    scopus 로고
    • Local homology recognition and distance measures in linear time using compressed amino acid alphabets
    • Edgar, R.C.: Local homology recognition and distance measures in linear time using compressed amino acid alphabets. Nucleic Acids Res 32 (2004) 380-385
    • (2004) Nucleic Acids Res , vol.32 , pp. 380-385
    • Edgar, R.C.1
  • 44
    • 85127836544 scopus 로고    scopus 로고
    • Discriminative training methods for hidden markov models: Theory and experiments with perceptron algorithms
    • Collins, M.: Discriminative training methods for hidden markov models: theory and experiments with perceptron algorithms. In: EMNLP. (2002)
    • (2002) EMNLP
    • Collins, M.1


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